Starting phenix.real_space_refine on Fri Sep 11 01:06:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7to2_26027/09_2026/7to2_26027.cif Found real_map, /net/cci-nas-00/data/ceres_data/7to2_26027/09_2026/7to2_26027.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7to2_26027/09_2026/7to2_26027.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7to2_26027/09_2026/7to2_26027.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7to2_26027/09_2026/7to2_26027.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7to2_26027/09_2026/7to2_26027.cif" model { file = "/net/cci-nas-00/data/ceres_data/7to2_26027/09_2026/7to2_26027.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7to2_26027/09_2026/7to2_26027.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 32 5.49 5 Mg 1 5.21 5 S 33 5.16 5 C 3733 2.51 5 N 1039 2.21 5 O 1213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6052 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5384 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 25, 'TRANS': 644} Chain breaks: 1 Chain: "B" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 639 Classifications: {'RNAv2': 30} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 15} Link IDs: {'rna3p': 29} Chain breaks: 1 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4570 SG CYS A 810 40.487 21.767 28.769 1.00 38.49 S ATOM 4596 SG CYS A 813 39.020 18.506 27.949 1.00 48.41 S ATOM 4908 SG CYS A 864 40.109 19.526 24.622 1.00 65.65 S ATOM 4947 SG CYS A 869 37.263 21.217 26.585 1.00 66.55 S Time building chain proxies: 1.35, per 1000 atoms: 0.22 Number of scatterers: 6052 At special positions: 0 Unit cell: (87.15, 97.65, 72.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 33 16.00 P 32 15.00 Mg 1 11.99 O 1213 8.00 N 1039 7.00 C 3733 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.42 Conformation dependent library (CDL) restraints added in 313.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 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 " Number of angles added : 6 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 48.8% alpha, 8.8% beta 15 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.621A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.572A pdb=" N VAL A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.656A pdb=" N GLU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.567A pdb=" N LEU A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 366 removed outlier: 3.833A pdb=" N ILE A 365 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.510A 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 374 through 377 Processing helix chain 'A' and resid 381 through 395 Processing helix chain 'A' and resid 419 through 434 Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.851A pdb=" N LEU A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 491 Processing helix chain 'A' and resid 492 through 496 removed outlier: 3.609A pdb=" N LEU A 496 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 521 removed outlier: 3.519A pdb=" N MET A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 556 Processing helix chain 'A' and resid 559 through 576 removed outlier: 3.609A pdb=" N ALA A 563 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 576 " --> pdb=" O SER A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 593 removed outlier: 3.935A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 602 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 636 through 649 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 720 through 729 Processing helix chain 'A' and resid 746 through 769 Processing helix chain 'A' and resid 772 through 792 Processing helix chain 'A' and resid 835 through 840 removed outlier: 3.524A pdb=" N LYS A 839 " --> pdb=" O GLY A 835 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A 840 " --> pdb=" O ASP A 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 840' Processing sheet with id=AA1, first strand: chain 'A' and resid 321 through 323 removed outlier: 6.958A pdb=" N THR A 322 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL A 293 " --> pdb=" O ILE A 344 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU A 346 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N PHE A 295 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET A 369 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU A 408 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N PHE A 371 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 462 removed outlier: 6.372A pdb=" N GLN A 457 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU A 740 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE A 459 " --> pdb=" O LEU A 740 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR A 742 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ARG A 461 " --> pdb=" O THR A 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 661 removed outlier: 6.336A pdb=" N GLY A 659 " --> pdb=" O ILE A 695 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819 removed outlier: 7.226A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 832 through 833 removed outlier: 4.455A pdb=" N ILE A 916 " --> pdb=" O VAL A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 844 removed outlier: 3.968A pdb=" N GLY A 874 " --> pdb=" O ILE A 862 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N CYS A 864 " --> pdb=" O ASP A 872 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ASP A 872 " --> pdb=" O CYS A 864 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 0.80 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1473 1.33 - 1.45: 1254 1.45 - 1.57: 3397 1.57 - 1.70: 61 1.70 - 1.82: 46 Bond restraints: 6231 Sorted by residual: bond pdb=" C4 ADP A1003 " pdb=" C5 ADP A1003 " ideal model delta sigma weight residual 1.490 1.394 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" N ILE A 337 " pdb=" CA ILE A 337 " ideal model delta sigma weight residual 1.458 1.490 -0.032 9.00e-03 1.23e+04 1.25e+01 bond pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.19e-02 7.06e+03 9.61e+00 bond pdb=" N VAL A 800 " pdb=" CA VAL A 800 " ideal model delta sigma weight residual 1.457 1.485 -0.028 9.00e-03 1.23e+04 9.47e+00 bond pdb=" N VAL A 699 " pdb=" CA VAL A 699 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.18e-02 7.18e+03 9.11e+00 ... (remaining 6226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 7467 1.82 - 3.64: 1056 3.64 - 5.46: 19 5.46 - 7.27: 6 7.27 - 9.09: 2 Bond angle restraints: 8550 Sorted by residual: angle pdb=" C PRO A 658 " pdb=" N GLY A 659 " pdb=" CA GLY A 659 " ideal model delta sigma weight residual 121.65 124.64 -2.99 6.80e-01 2.16e+00 1.93e+01 angle pdb=" N1 ADP A1003 " pdb=" C2 ADP A1003 " pdb=" N3 ADP A1003 " ideal model delta sigma weight residual 120.00 129.09 -9.09 3.00e+00 1.11e-01 9.19e+00 angle pdb=" N ILE A 467 " pdb=" CA ILE A 467 " pdb=" C ILE A 467 " ideal model delta sigma weight residual 111.90 109.57 2.33 8.10e-01 1.52e+00 8.27e+00 angle pdb=" CA LYS A 528 " pdb=" C LYS A 528 " pdb=" O LYS A 528 " ideal model delta sigma weight residual 120.70 117.78 2.92 1.03e+00 9.43e-01 8.03e+00 angle pdb=" CA GLY A 659 " pdb=" C GLY A 659 " pdb=" O GLY A 659 " ideal model delta sigma weight residual 120.94 118.73 2.21 7.80e-01 1.64e+00 8.03e+00 ... (remaining 8545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 3355 16.18 - 32.37: 268 32.37 - 48.55: 81 48.55 - 64.73: 17 64.73 - 80.91: 8 Dihedral angle restraints: 3729 sinusoidal: 1764 harmonic: 1965 Sorted by residual: dihedral pdb=" O5' A B 57 " pdb=" C5' A B 57 " pdb=" C4' A B 57 " pdb=" C3' A B 57 " ideal model delta sinusoidal sigma weight residual -180.00 -158.23 -21.77 3 6.40e+00 2.44e-02 1.52e+01 dihedral pdb=" O5' C B 9 " pdb=" C5' C B 9 " pdb=" C4' C B 9 " pdb=" C3' C B 9 " ideal model delta sinusoidal sigma weight residual 60.00 38.63 21.37 3 6.40e+00 2.44e-02 1.47e+01 dihedral pdb=" O5' U B 8 " pdb=" C5' U B 8 " pdb=" C4' U B 8 " pdb=" C3' U B 8 " ideal model delta sinusoidal sigma weight residual -180.00 -160.12 -19.88 3 6.40e+00 2.44e-02 1.29e+01 ... (remaining 3726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 491 0.055 - 0.110: 340 0.110 - 0.165: 115 0.165 - 0.220: 29 0.220 - 0.275: 4 Chirality restraints: 979 Sorted by residual: chirality pdb=" P G B 6 " pdb=" OP1 G B 6 " pdb=" OP2 G B 6 " pdb=" O5' G B 6 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" P C B 13 " pdb=" OP1 C B 13 " pdb=" OP2 C B 13 " pdb=" O5' C B 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" P C B 46 " pdb=" OP1 C B 46 " pdb=" OP2 C B 46 " pdb=" O5' C B 46 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 976 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 10 " -0.026 2.00e-02 2.50e+03 9.93e-03 2.96e+00 pdb=" N9 G B 10 " 0.015 2.00e-02 2.50e+03 pdb=" C8 G B 10 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G B 10 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G B 10 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 10 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 10 " -0.012 2.00e-02 2.50e+03 pdb=" N1 G B 10 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 10 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 10 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 490 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C CYS A 490 " -0.028 2.00e-02 2.50e+03 pdb=" O CYS A 490 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS A 491 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADP A1003 " 0.011 2.00e-02 2.50e+03 9.35e-03 2.40e+00 pdb=" C2 ADP A1003 " 0.012 2.00e-02 2.50e+03 pdb=" C4 ADP A1003 " -0.002 2.00e-02 2.50e+03 pdb=" C5 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" C6 ADP A1003 " -0.003 2.00e-02 2.50e+03 pdb=" C8 ADP A1003 " 0.015 2.00e-02 2.50e+03 pdb=" N1 ADP A1003 " 0.003 2.00e-02 2.50e+03 pdb=" N3 ADP A1003 " -0.013 2.00e-02 2.50e+03 pdb=" N6 ADP A1003 " 0.006 2.00e-02 2.50e+03 pdb=" N7 ADP A1003 " -0.008 2.00e-02 2.50e+03 pdb=" N9 ADP A1003 " -0.013 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1185 2.81 - 3.33: 5962 3.33 - 3.85: 10226 3.85 - 4.38: 11711 4.38 - 4.90: 19769 Nonbonded interactions: 48853 Sorted by model distance: nonbonded pdb=" O SER A 378 " pdb=" ND2 ASN A 384 " model vdw 2.284 3.120 nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.296 3.040 nonbonded pdb=" O THR A 662 " pdb=" NE2 GLN A 678 " model vdw 2.334 3.120 nonbonded pdb=" O ASP A 690 " pdb=" ND1 HIS A 691 " model vdw 2.348 3.120 nonbonded pdb=" O SER A 698 " pdb=" OG SER A 698 " model vdw 2.353 3.040 ... (remaining 48848 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: 0.440 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.460 Find NCS groups from input model: 0.030 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 : 0.011 0.142 6235 Z= 0.805 Angle : 1.263 38.796 8556 Z= 0.824 Chirality : 0.078 0.275 979 Planarity : 0.004 0.016 979 Dihedral : 13.366 80.913 2453 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.84 % Allowed : 6.86 % Favored : 92.31 % 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: -1.96 (0.30), residues: 666 helix: 0.75 (0.28), residues: 298 sheet: -3.26 (0.49), residues: 75 loop : -3.04 (0.29), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 461 TYR 0.012 0.003 TYR A 548 PHE 0.011 0.003 PHE A 460 TRP 0.008 0.002 TRP A 771 HIS 0.005 0.001 HIS A 782 Details of bonding type rmsd/Z covalent geometry : bond 0.01074 / 0.80 ( 6231) covalent geometry : angle 1.15304 / 0.82 ( 8550) hydrogen bonds : bond 0.11541 / 6.96 ( 275) hydrogen bonds : angle 4.21036 / 2.94 ( 768) metal coordination : bond 0.13212 / 7.88 ( 4) metal coordination : angle 19.52163 / 10.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.233 Fit side-chains REVERT: A 457 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7624 (tp-100) outliers start: 5 outliers final: 3 residues processed: 94 average time/residue: 0.0801 time to fit residues: 9.8897 Evaluate side-chains 60 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 457 GLN Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 775 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN A 375 HIS ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 477 GLN A 500 GLN A 769 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.093851 restraints weight = 8371.681| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.37 r_work: 0.2978 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6235 Z= 0.127 Angle : 0.567 7.219 8556 Z= 0.255 Chirality : 0.044 0.207 979 Planarity : 0.003 0.025 979 Dihedral : 9.416 56.953 1089 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.67 % Allowed : 12.54 % Favored : 85.79 % 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: -0.96 (0.32), residues: 666 helix: 1.72 (0.29), residues: 309 sheet: -3.01 (0.51), residues: 76 loop : -2.78 (0.30), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 728 TYR 0.007 0.001 TYR A 246 PHE 0.006 0.001 PHE A 918 TRP 0.004 0.001 TRP A 512 HIS 0.002 0.000 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6231) covalent geometry : angle 0.55650 / 0.25 ( 8550) hydrogen bonds : bond 0.03265 / 2.12 ( 275) hydrogen bonds : angle 3.02340 / 2.08 ( 768) metal coordination : bond 0.00824 / 0.56 ( 4) metal coordination : angle 4.05351 / 2.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.255 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.0599 time to fit residues: 6.3844 Evaluate side-chains 63 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 691 HIS Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 0.0040 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.093313 restraints weight = 8244.460| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.35 r_work: 0.2974 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6235 Z= 0.126 Angle : 0.554 6.401 8556 Z= 0.250 Chirality : 0.043 0.187 979 Planarity : 0.003 0.028 979 Dihedral : 9.175 56.385 1085 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.01 % Allowed : 14.21 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.32), residues: 666 helix: 2.16 (0.29), residues: 305 sheet: -2.62 (0.59), residues: 64 loop : -2.41 (0.30), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 461 TYR 0.014 0.001 TYR A 473 PHE 0.005 0.001 PHE A 371 TRP 0.003 0.000 TRP A 512 HIS 0.002 0.000 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 6231) covalent geometry : angle 0.54670 / 0.25 ( 8550) hydrogen bonds : bond 0.03173 / 2.07 ( 275) hydrogen bonds : angle 2.98411 / 2.05 ( 768) metal coordination : bond 0.00624 / 0.42 ( 4) metal coordination : angle 3.46706 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.208 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 74 average time/residue: 0.0553 time to fit residues: 6.0069 Evaluate side-chains 62 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 0.0070 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 0.0070 chunk 61 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** 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 = 0.3420 r_free = 0.3420 target = 0.116758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094972 restraints weight = 8214.390| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.33 r_work: 0.3003 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6235 Z= 0.101 Angle : 0.537 5.733 8556 Z= 0.243 Chirality : 0.043 0.194 979 Planarity : 0.003 0.030 979 Dihedral : 9.059 58.831 1083 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.84 % Allowed : 15.55 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.33), residues: 666 helix: 2.38 (0.29), residues: 305 sheet: -2.50 (0.54), residues: 76 loop : -2.34 (0.32), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 461 TYR 0.012 0.001 TYR A 473 PHE 0.006 0.001 PHE A 371 TRP 0.003 0.000 TRP A 512 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 6231) covalent geometry : angle 0.53228 / 0.24 ( 8550) hydrogen bonds : bond 0.03017 / 1.97 ( 275) hydrogen bonds : angle 2.91744 / 1.99 ( 768) metal coordination : bond 0.00499 / 0.34 ( 4) metal coordination : angle 2.82605 / 1.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 883 GLU cc_start: 0.8548 (tt0) cc_final: 0.8333 (tt0) outliers start: 11 outliers final: 7 residues processed: 72 average time/residue: 0.0511 time to fit residues: 5.4102 Evaluate side-chains 64 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 287 GLN ** A 393 GLN ** 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 = 0.3383 r_free = 0.3383 target = 0.113733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.091875 restraints weight = 8338.868| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.32 r_work: 0.2951 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6235 Z= 0.147 Angle : 0.566 5.701 8556 Z= 0.258 Chirality : 0.043 0.168 979 Planarity : 0.003 0.030 979 Dihedral : 8.988 59.012 1083 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.67 % Allowed : 16.39 % Favored : 81.94 % 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: -0.01 (0.33), residues: 666 helix: 2.40 (0.29), residues: 306 sheet: -2.33 (0.61), residues: 64 loop : -2.21 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 488 TYR 0.014 0.001 TYR A 473 PHE 0.007 0.001 PHE A 295 TRP 0.002 0.000 TRP A 512 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 6231) covalent geometry : angle 0.56217 / 0.26 ( 8550) hydrogen bonds : bond 0.03263 / 2.15 ( 275) hydrogen bonds : angle 3.01752 / 2.07 ( 768) metal coordination : bond 0.00586 / 0.39 ( 4) metal coordination : angle 2.58511 / 1.48 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.253 Fit side-chains REVERT: A 339 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8227 (tm-30) REVERT: A 878 LYS cc_start: 0.8134 (tmtt) cc_final: 0.7391 (tmtt) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.0501 time to fit residues: 4.8627 Evaluate side-chains 62 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 56 optimal weight: 0.0030 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** 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 = 0.3421 r_free = 0.3421 target = 0.117104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095515 restraints weight = 8339.618| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.33 r_work: 0.2984 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6235 Z= 0.105 Angle : 0.547 5.824 8556 Z= 0.249 Chirality : 0.043 0.183 979 Planarity : 0.003 0.031 979 Dihedral : 9.038 61.415 1083 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.84 % Allowed : 16.89 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.33), residues: 666 helix: 2.56 (0.29), residues: 306 sheet: -2.25 (0.62), residues: 64 loop : -2.14 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.010 0.001 TYR A 473 PHE 0.006 0.001 PHE A 371 TRP 0.003 0.000 TRP A 873 HIS 0.002 0.000 HIS A 876 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 6231) covalent geometry : angle 0.54344 / 0.25 ( 8550) hydrogen bonds : bond 0.03088 / 2.03 ( 275) hydrogen bonds : angle 2.93840 / 2.01 ( 768) metal coordination : bond 0.00425 / 0.29 ( 4) metal coordination : angle 2.34301 / 1.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.141 Fit side-chains REVERT: A 339 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8225 (tm-30) outliers start: 17 outliers final: 10 residues processed: 71 average time/residue: 0.0517 time to fit residues: 5.4601 Evaluate side-chains 65 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 26 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 0.0020 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093432 restraints weight = 8394.611| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.33 r_work: 0.2949 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6235 Z= 0.143 Angle : 0.574 7.333 8556 Z= 0.263 Chirality : 0.043 0.165 979 Planarity : 0.003 0.031 979 Dihedral : 8.974 60.811 1083 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.17 % Allowed : 16.89 % Favored : 80.94 % 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 (0.33), residues: 666 helix: 2.59 (0.29), residues: 306 sheet: -2.14 (0.63), residues: 64 loop : -2.10 (0.32), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.012 0.001 TYR A 473 PHE 0.006 0.001 PHE A 295 TRP 0.002 0.000 TRP A 512 HIS 0.002 0.001 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 6231) covalent geometry : angle 0.57116 / 0.26 ( 8550) hydrogen bonds : bond 0.03255 / 2.16 ( 275) hydrogen bonds : angle 3.01194 / 2.07 ( 768) metal coordination : bond 0.00508 / 0.33 ( 4) metal coordination : angle 2.19123 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.138 Fit side-chains REVERT: A 339 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8177 (tm-30) REVERT: A 834 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8401 (tp) REVERT: A 878 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7295 (tmtt) outliers start: 13 outliers final: 8 residues processed: 65 average time/residue: 0.0524 time to fit residues: 5.0428 Evaluate side-chains 64 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** 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 = 0.3399 r_free = 0.3399 target = 0.115458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093632 restraints weight = 8400.806| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.33 r_work: 0.2958 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6235 Z= 0.130 Angle : 0.571 6.640 8556 Z= 0.263 Chirality : 0.043 0.171 979 Planarity : 0.003 0.033 979 Dihedral : 8.987 61.972 1083 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.01 % Allowed : 17.73 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.33), residues: 666 helix: 2.60 (0.29), residues: 306 sheet: -2.09 (0.64), residues: 64 loop : -2.05 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.012 0.001 TYR A 473 PHE 0.005 0.001 PHE A 371 TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 6231) covalent geometry : angle 0.56795 / 0.26 ( 8550) hydrogen bonds : bond 0.03193 / 2.11 ( 275) hydrogen bonds : angle 2.99498 / 2.06 ( 768) metal coordination : bond 0.00492 / 0.32 ( 4) metal coordination : angle 2.32432 / 1.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.148 Fit side-chains REVERT: A 339 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8197 (tm-30) REVERT: A 834 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8414 (tp) REVERT: A 878 LYS cc_start: 0.7903 (tmtt) cc_final: 0.7072 (tmtt) outliers start: 12 outliers final: 9 residues processed: 63 average time/residue: 0.0556 time to fit residues: 5.2343 Evaluate side-chains 64 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 0.0020 chunk 54 optimal weight: 3.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** 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 = 0.3425 r_free = 0.3425 target = 0.117151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095759 restraints weight = 8402.489| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.31 r_work: 0.2986 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6235 Z= 0.103 Angle : 0.559 7.161 8556 Z= 0.256 Chirality : 0.043 0.202 979 Planarity : 0.003 0.033 979 Dihedral : 8.981 63.738 1083 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.34 % Allowed : 18.23 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.33), residues: 666 helix: 2.68 (0.29), residues: 306 sheet: -1.99 (0.65), residues: 64 loop : -1.99 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.013 0.001 TYR A 473 PHE 0.005 0.001 PHE A 371 TRP 0.003 0.000 TRP A 512 HIS 0.001 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 6231) covalent geometry : angle 0.55579 / 0.26 ( 8550) hydrogen bonds : bond 0.03065 / 2.03 ( 275) hydrogen bonds : angle 2.90380 / 1.99 ( 768) metal coordination : bond 0.00412 / 0.27 ( 4) metal coordination : angle 2.15608 / 1.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.217 Fit side-chains REVERT: A 339 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8247 (tm-30) REVERT: A 878 LYS cc_start: 0.7863 (tmtt) cc_final: 0.7080 (tmtt) outliers start: 8 outliers final: 8 residues processed: 60 average time/residue: 0.0595 time to fit residues: 5.2666 Evaluate side-chains 62 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** 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 = 0.3424 r_free = 0.3424 target = 0.117094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095748 restraints weight = 8344.338| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.31 r_work: 0.2986 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6235 Z= 0.111 Angle : 0.571 8.753 8556 Z= 0.262 Chirality : 0.043 0.196 979 Planarity : 0.003 0.035 979 Dihedral : 8.977 64.067 1083 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.84 % Allowed : 17.56 % Favored : 80.60 % 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: 0.44 (0.34), residues: 666 helix: 2.72 (0.29), residues: 306 sheet: -1.89 (0.66), residues: 64 loop : -1.96 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.016 0.001 TYR A 473 PHE 0.005 0.001 PHE A 579 TRP 0.002 0.000 TRP A 512 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 6231) covalent geometry : angle 0.56850 / 0.26 ( 8550) hydrogen bonds : bond 0.03058 / 2.03 ( 275) hydrogen bonds : angle 2.88845 / 1.98 ( 768) metal coordination : bond 0.00419 / 0.28 ( 4) metal coordination : angle 2.18305 / 1.25 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.193 Fit side-chains REVERT: A 339 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8290 (tm-30) REVERT: A 878 LYS cc_start: 0.7891 (tmtt) cc_final: 0.7105 (tmtt) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.0577 time to fit residues: 5.2831 Evaluate side-chains 63 residues out of total 598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 525 MET Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 882 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 44 optimal weight: 0.0060 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 50.0000 chunk 9 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 14 optimal weight: 0.7980 overall best weight: 0.3072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 393 GLN ** 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 = 0.3450 r_free = 0.3450 target = 0.118867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.096837 restraints weight = 8223.652| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.34 r_work: 0.3028 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6235 Z= 0.094 Angle : 0.561 8.452 8556 Z= 0.255 Chirality : 0.043 0.194 979 Planarity : 0.003 0.034 979 Dihedral : 8.980 66.346 1083 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.51 % Allowed : 18.06 % Favored : 80.43 % 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: 0.55 (0.34), residues: 666 helix: 2.80 (0.29), residues: 306 sheet: -1.78 (0.67), residues: 64 loop : -1.91 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 488 TYR 0.016 0.001 TYR A 473 PHE 0.005 0.001 PHE A 579 TRP 0.003 0.000 TRP A 771 HIS 0.002 0.000 HIS A 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 6231) covalent geometry : angle 0.55714 / 0.26 ( 8550) hydrogen bonds : bond 0.02950 / 1.96 ( 275) hydrogen bonds : angle 2.79055 / 1.91 ( 768) metal coordination : bond 0.00361 / 0.24 ( 4) metal coordination : angle 2.38929 / 1.39 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.20 seconds wall clock time: 24 minutes 25.10 seconds (1465.10 seconds total)