Starting phenix.real_space_refine on Wed Aug 5 04:23:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2i_38856/08_2026/8y2i_38856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2i_38856/08_2026/8y2i_38856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y2i_38856/08_2026/8y2i_38856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2i_38856/08_2026/8y2i_38856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y2i_38856/08_2026/8y2i_38856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2i_38856/08_2026/8y2i_38856.map" } resolution = 2.92 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= -0.002 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 143 5.49 5 S 20 5.16 5 C 4960 2.51 5 N 1577 2.21 5 O 1976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8676 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 587 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "D" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 210 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 5671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5671 Classifications: {'peptide': 723} Link IDs: {'PTRANS': 35, 'TRANS': 687} Chain breaks: 4 Chain: "C" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2208 Classifications: {'RNA': 104} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 46, 'rna3p_pyr': 46} Link IDs: {'rna2p': 12, 'rna3p': 91} Chain breaks: 1 Time building chain proxies: 1.98, per 1000 atoms: 0.23 Number of scatterers: 8676 At special positions: 0 Unit cell: (109.08, 93.96, 112.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 143 15.00 O 1976 8.00 N 1577 7.00 C 4960 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: 1.01 Conformation dependent library (CDL) restraints added in 252.5 milliseconds 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 4 sheets defined 48.8% alpha, 12.3% beta 43 base pairs and 89 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.667A pdb=" N HIS A 19 " --> pdb=" O ALA A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 81 removed outlier: 3.959A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.657A pdb=" N LYS A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 removed outlier: 3.888A pdb=" N TRP A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 162 removed outlier: 4.125A pdb=" N GLY A 134 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLY A 135 " --> pdb=" O ASP A 131 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY A 136 " --> pdb=" O ASN A 132 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 185 through 189 removed outlier: 4.296A pdb=" N LEU A 189 " --> pdb=" O PHE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 211 removed outlier: 3.708A pdb=" N TRP A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 removed outlier: 3.821A pdb=" N LYS A 215 " --> pdb=" O LEU A 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 246 through 265 removed outlier: 3.649A pdb=" N ALA A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 267 No H-bonds generated for 'chain 'A' and resid 266 through 267' Processing helix chain 'A' and resid 268 through 272 removed outlier: 3.767A pdb=" N LYS A 271 " --> pdb=" O ARG A 268 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 272 " --> pdb=" O PHE A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 272' Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 300 through 316 removed outlier: 4.301A pdb=" N ALA A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ALA A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLN A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 333 removed outlier: 3.651A pdb=" N LEU A 324 " --> pdb=" O GLN A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 Processing helix chain 'A' and resid 350 through 369 Processing helix chain 'A' and resid 369 through 376 Processing helix chain 'A' and resid 379 through 399 Proline residue: A 387 - end of helix Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.792A pdb=" N GLU A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 551 Processing helix chain 'A' and resid 635 through 658 removed outlier: 3.897A pdb=" N ALA A 641 " --> pdb=" O ASN A 637 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU A 642 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU A 645 " --> pdb=" O ALA A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 698 removed outlier: 3.556A pdb=" N MET A 688 " --> pdb=" O GLN A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 removed outlier: 3.552A pdb=" N GLU A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 884 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 43 removed outlier: 6.609A pdb=" N ASP A 552 " --> pdb=" O ARG A 541 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG A 541 " --> pdb=" O ASP A 552 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR A 554 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU A 539 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N THR A 556 " --> pdb=" O GLY A 537 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 537 " --> pdb=" O THR A 556 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR A 558 " --> pdb=" O GLY A 535 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 455 Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 455 removed outlier: 4.835A pdb=" N LEU A 428 " --> pdb=" O PHE A 473 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N SER A 475 " --> pdb=" O GLY A 426 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N GLY A 426 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 600 removed outlier: 7.262A pdb=" N LEU A 596 " --> pdb=" O ASP A 591 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP A 591 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE A 662 " --> pdb=" O LYS A 573 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE A 575 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA A 664 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 9.067A pdb=" N ILE A 577 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 661 " --> pdb=" O LYS A 719 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 721 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU A 663 " --> pdb=" O VAL A 721 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 115 hydrogen bonds 220 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 89 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1077 1.29 - 1.42: 3154 1.42 - 1.55: 4606 1.55 - 1.68: 280 1.68 - 1.81: 32 Bond restraints: 9149 Sorted by residual: bond pdb=" C GLU A 370 " pdb=" O GLU A 370 " ideal model delta sigma weight residual 1.244 1.167 0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C LYS A 356 " pdb=" O LYS A 356 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.26e-02 6.30e+03 3.58e+01 bond pdb=" CA GLY A 413 " pdb=" C GLY A 413 " ideal model delta sigma weight residual 1.512 1.454 0.058 1.15e-02 7.56e+03 2.50e+01 bond pdb=" O3' G C 0 " pdb=" P A C 1 " ideal model delta sigma weight residual 1.607 1.548 0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" O3' G C 2 " pdb=" P G C 3 " ideal model delta sigma weight residual 1.607 1.550 0.057 1.20e-02 6.94e+03 2.24e+01 ... (remaining 9144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 12396 2.01 - 4.02: 551 4.02 - 6.04: 55 6.04 - 8.05: 11 8.05 - 10.06: 6 Bond angle restraints: 13019 Sorted by residual: angle pdb=" N ARG A 334 " pdb=" CA ARG A 334 " pdb=" C ARG A 334 " ideal model delta sigma weight residual 113.16 103.10 10.06 1.24e+00 6.50e-01 6.58e+01 angle pdb=" O4' A C -11 " pdb=" C4' A C -11 " pdb=" C3' A C -11 " ideal model delta sigma weight residual 106.10 100.44 5.66 8.00e-01 1.56e+00 5.00e+01 angle pdb=" N ASP A 156 " pdb=" CA ASP A 156 " pdb=" C ASP A 156 " ideal model delta sigma weight residual 111.14 104.53 6.61 1.08e+00 8.57e-01 3.75e+01 angle pdb=" N ASN A 45 " pdb=" CA ASN A 45 " pdb=" CB ASN A 45 " ideal model delta sigma weight residual 110.57 118.62 -8.05 1.35e+00 5.49e-01 3.56e+01 angle pdb=" C THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta sigma weight residual 110.79 120.66 -9.87 1.66e+00 3.63e-01 3.54e+01 ... (remaining 13014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 4658 21.21 - 42.42: 548 42.42 - 63.63: 257 63.63 - 84.84: 74 84.84 - 106.05: 9 Dihedral angle restraints: 5546 sinusoidal: 3475 harmonic: 2071 Sorted by residual: dihedral pdb=" C THR A 412 " pdb=" N THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta harmonic sigma weight residual -122.00 -137.57 15.57 0 2.50e+00 1.60e-01 3.88e+01 dihedral pdb=" N THR A 412 " pdb=" C THR A 412 " pdb=" CA THR A 412 " pdb=" CB THR A 412 " ideal model delta harmonic sigma weight residual 123.40 134.44 -11.04 0 2.50e+00 1.60e-01 1.95e+01 dihedral pdb=" O4' U C-100 " pdb=" C1' U C-100 " pdb=" N1 U C-100 " pdb=" C2 U C-100 " ideal model delta sinusoidal sigma weight residual 232.00 167.57 64.43 1 1.70e+01 3.46e-03 1.89e+01 ... (remaining 5543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1342 0.098 - 0.196: 153 0.196 - 0.294: 6 0.294 - 0.392: 2 0.392 - 0.490: 1 Chirality restraints: 1504 Sorted by residual: chirality pdb=" CA THR A 412 " pdb=" N THR A 412 " pdb=" C THR A 412 " pdb=" CB THR A 412 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 6.01e+00 chirality pdb=" C1' DT D -4 " pdb=" O4' DT D -4 " pdb=" C2' DT D -4 " pdb=" N1 DT D -4 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C1' DT D -5 " pdb=" O4' DT D -5 " pdb=" C2' DT D -5 " pdb=" N1 DT D -5 " both_signs ideal model delta sigma weight residual False 2.43 2.05 0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 1501 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 731 " 0.026 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C SER A 731 " -0.088 2.00e-02 2.50e+03 pdb=" O SER A 731 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA A 732 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 385 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C GLU A 385 " -0.070 2.00e-02 2.50e+03 pdb=" O GLU A 385 " 0.026 2.00e-02 2.50e+03 pdb=" N THR A 386 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 684 " -0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C GLN A 684 " 0.065 2.00e-02 2.50e+03 pdb=" O GLN A 684 " -0.024 2.00e-02 2.50e+03 pdb=" N TYR A 685 " -0.023 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1391 2.75 - 3.29: 8245 3.29 - 3.83: 16412 3.83 - 4.36: 19783 4.36 - 4.90: 29550 Nonbonded interactions: 75381 Sorted by model distance: nonbonded pdb=" N ARG A 240 " pdb=" OP1 G C 6 " model vdw 2.219 3.120 nonbonded pdb=" O CYS A 91 " pdb=" OG SER A 92 " model vdw 2.221 3.040 nonbonded pdb=" OP1 DA B 23 " pdb=" NZ LYS A 488 " model vdw 2.236 3.120 nonbonded pdb=" O GLU A 440 " pdb=" O4 U C-101 " model vdw 2.257 3.040 nonbonded pdb=" OE1 GLN A 878 " pdb=" NZ LYS A 882 " model vdw 2.271 3.120 ... (remaining 75376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 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 : 0.006 0.076 9149 Z= 0.447 Angle : 0.876 10.060 13019 Z= 0.660 Chirality : 0.057 0.490 1504 Planarity : 0.006 0.057 1162 Dihedral : 21.145 106.055 4214 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 0.71 % Allowed : 1.07 % Favored : 98.22 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.31), residues: 713 helix: -0.72 (0.28), residues: 320 sheet: -1.56 (0.48), residues: 100 loop : -2.45 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 874 TYR 0.017 0.002 TYR A 241 PHE 0.036 0.002 PHE A 717 TRP 0.016 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.45 ( 9149) covalent geometry : angle 0.87561 / 0.66 (13019) hydrogen bonds : bond 0.12353 / 14.13 ( 392) hydrogen bonds : angle 6.36460 / 8.75 ( 1024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.223 Fit side-chains REVERT: A 22 GLN cc_start: 0.7509 (mt0) cc_final: 0.7156 (mm110) REVERT: A 90 LYS cc_start: 0.6715 (ptpt) cc_final: 0.6354 (pptt) REVERT: A 239 GLN cc_start: 0.7085 (tm-30) cc_final: 0.6733 (tm-30) REVERT: A 262 TYR cc_start: 0.8103 (t80) cc_final: 0.7790 (t80) REVERT: A 384 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6361 (mt-10) REVERT: A 390 LYS cc_start: 0.6322 (mmtt) cc_final: 0.5923 (tppt) REVERT: A 410 GLN cc_start: 0.6034 (OUTLIER) cc_final: 0.5683 (tt0) REVERT: A 693 GLU cc_start: 0.7223 (mt-10) cc_final: 0.7012 (mt-10) REVERT: A 850 ARG cc_start: 0.6083 (mtt-85) cc_final: 0.4647 (mtt-85) REVERT: A 851 LYS cc_start: 0.6813 (tttp) cc_final: 0.6474 (tptp) outliers start: 4 outliers final: 2 residues processed: 108 average time/residue: 0.7298 time to fit residues: 83.0179 Evaluate side-chains 80 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 GLN ** A 684 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 = 0.4687 r_free = 0.4687 target = 0.249893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.216788 restraints weight = 9546.960| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 2.03 r_work: 0.4011 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9149 Z= 0.174 Angle : 0.644 7.082 13019 Z= 0.361 Chirality : 0.040 0.183 1504 Planarity : 0.006 0.091 1162 Dihedral : 22.081 103.405 2845 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 3.02 % Allowed : 11.72 % Favored : 85.26 % 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: -1.69 (0.31), residues: 713 helix: -0.08 (0.29), residues: 324 sheet: -1.35 (0.51), residues: 98 loop : -2.20 (0.37), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 855 TYR 0.019 0.002 TYR A 725 PHE 0.017 0.002 PHE A 717 TRP 0.017 0.002 TRP A 520 HIS 0.010 0.001 HIS A 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 ( 9149) covalent geometry : angle 0.64372 / 0.36 (13019) hydrogen bonds : bond 0.05320 / 5.64 ( 392) hydrogen bonds : angle 5.02843 / 6.93 ( 1024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.250 Fit side-chains REVERT: A 22 GLN cc_start: 0.7412 (mt0) cc_final: 0.7059 (mm110) REVERT: A 90 LYS cc_start: 0.6733 (ptpt) cc_final: 0.6225 (pptt) REVERT: A 133 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6976 (mtt) REVERT: A 155 TYR cc_start: 0.7556 (t80) cc_final: 0.7120 (t80) REVERT: A 197 TYR cc_start: 0.6597 (t80) cc_final: 0.6192 (t80) REVERT: A 262 TYR cc_start: 0.8062 (t80) cc_final: 0.7715 (t80) REVERT: A 340 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.5728 (tttm) REVERT: A 384 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6409 (mt-10) REVERT: A 390 LYS cc_start: 0.6455 (mmtt) cc_final: 0.5728 (ptmm) REVERT: A 410 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.6350 (tt0) REVERT: A 489 LYS cc_start: 0.7970 (ptpp) cc_final: 0.7678 (pttt) REVERT: A 636 ARG cc_start: 0.6807 (mmt180) cc_final: 0.6493 (mmm-85) REVERT: A 683 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6230 (tpt) REVERT: A 693 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7031 (mt-10) REVERT: A 698 GLU cc_start: 0.7383 (tt0) cc_final: 0.6833 (tt0) REVERT: A 850 ARG cc_start: 0.6067 (mtt-85) cc_final: 0.4878 (mtt-85) REVERT: A 851 LYS cc_start: 0.6582 (tttp) cc_final: 0.6278 (tptt) REVERT: A 855 ARG cc_start: 0.5196 (tpp-160) cc_final: 0.4522 (tmm160) outliers start: 17 outliers final: 4 residues processed: 91 average time/residue: 0.7202 time to fit residues: 69.2316 Evaluate side-chains 78 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 683 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 0.0470 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 GLN ** A 451 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 = 0.4692 r_free = 0.4692 target = 0.250873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.218843 restraints weight = 9492.387| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 1.95 r_work: 0.4040 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9149 Z= 0.153 Angle : 0.591 6.274 13019 Z= 0.333 Chirality : 0.037 0.177 1504 Planarity : 0.005 0.061 1162 Dihedral : 22.014 101.233 2844 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.62 % Allowed : 13.32 % Favored : 82.06 % 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: -1.43 (0.31), residues: 713 helix: 0.09 (0.28), residues: 328 sheet: -1.29 (0.49), residues: 98 loop : -2.00 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 687 TYR 0.017 0.002 TYR A 241 PHE 0.019 0.002 PHE A 717 TRP 0.016 0.002 TRP A 520 HIS 0.006 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 ( 9149) covalent geometry : angle 0.59084 / 0.33 (13019) hydrogen bonds : bond 0.04816 / 5.07 ( 392) hydrogen bonds : angle 4.72864 / 6.55 ( 1024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.253 Fit side-chains REVERT: A 22 GLN cc_start: 0.7395 (mt0) cc_final: 0.7020 (mm110) REVERT: A 90 LYS cc_start: 0.6739 (ptpt) cc_final: 0.6257 (pptt) REVERT: A 133 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6893 (mtt) REVERT: A 153 LYS cc_start: 0.7972 (tmmt) cc_final: 0.7630 (ttpp) REVERT: A 155 TYR cc_start: 0.7530 (t80) cc_final: 0.7218 (t80) REVERT: A 197 TYR cc_start: 0.6603 (t80) cc_final: 0.6237 (t80) REVERT: A 262 TYR cc_start: 0.8059 (t80) cc_final: 0.7762 (t80) REVERT: A 303 GLN cc_start: 0.7855 (mt0) cc_final: 0.7617 (mt0) REVERT: A 328 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6557 (mt) REVERT: A 340 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.5527 (tttm) REVERT: A 369 LEU cc_start: 0.8108 (mt) cc_final: 0.7893 (mt) REVERT: A 384 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6616 (mt-10) REVERT: A 390 LYS cc_start: 0.6306 (mmtt) cc_final: 0.5990 (tppt) REVERT: A 410 GLN cc_start: 0.6897 (OUTLIER) cc_final: 0.6326 (tt0) REVERT: A 489 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7581 (pttp) REVERT: A 636 ARG cc_start: 0.6866 (mmt180) cc_final: 0.6581 (mmm-85) REVERT: A 683 MET cc_start: 0.6694 (OUTLIER) cc_final: 0.6328 (tpt) REVERT: A 698 GLU cc_start: 0.7429 (tt0) cc_final: 0.6796 (tt0) REVERT: A 851 LYS cc_start: 0.6562 (tttp) cc_final: 0.6236 (tptt) REVERT: A 855 ARG cc_start: 0.5323 (tpp-160) cc_final: 0.4675 (tmm160) outliers start: 26 outliers final: 6 residues processed: 94 average time/residue: 0.6633 time to fit residues: 66.0527 Evaluate side-chains 85 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 0.0770 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4693 r_free = 0.4693 target = 0.250892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.218526 restraints weight = 9576.528| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 2.02 r_work: 0.4024 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9149 Z= 0.154 Angle : 0.592 6.550 13019 Z= 0.331 Chirality : 0.037 0.172 1504 Planarity : 0.005 0.089 1162 Dihedral : 21.999 100.798 2844 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 5.15 % Allowed : 13.68 % Favored : 81.17 % 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: -1.31 (0.32), residues: 713 helix: 0.23 (0.29), residues: 327 sheet: -1.28 (0.49), residues: 99 loop : -1.97 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 687 TYR 0.016 0.002 TYR A 725 PHE 0.023 0.002 PHE A 717 TRP 0.016 0.002 TRP A 520 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 9149) covalent geometry : angle 0.59228 / 0.33 (13019) hydrogen bonds : bond 0.04753 / 4.94 ( 392) hydrogen bonds : angle 4.64775 / 6.42 ( 1024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.235 Fit side-chains REVERT: A 22 GLN cc_start: 0.7438 (mt0) cc_final: 0.7063 (mm110) REVERT: A 90 LYS cc_start: 0.6713 (ptpt) cc_final: 0.6242 (pptt) REVERT: A 133 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6860 (mtt) REVERT: A 153 LYS cc_start: 0.8010 (tmmt) cc_final: 0.7683 (ttpp) REVERT: A 155 TYR cc_start: 0.7564 (t80) cc_final: 0.7263 (t80) REVERT: A 197 TYR cc_start: 0.6608 (t80) cc_final: 0.6298 (t80) REVERT: A 262 TYR cc_start: 0.8022 (t80) cc_final: 0.7588 (t80) REVERT: A 303 GLN cc_start: 0.7883 (mt0) cc_final: 0.7626 (mt0) REVERT: A 333 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7698 (mm) REVERT: A 340 LYS cc_start: 0.7565 (OUTLIER) cc_final: 0.5315 (tttm) REVERT: A 384 GLU cc_start: 0.6897 (mm-30) cc_final: 0.6625 (mt-10) REVERT: A 390 LYS cc_start: 0.6338 (mmtt) cc_final: 0.5896 (tppt) REVERT: A 410 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: A 489 LYS cc_start: 0.8020 (ptpp) cc_final: 0.7604 (pttp) REVERT: A 500 LYS cc_start: 0.7230 (mtpp) cc_final: 0.6897 (pmmt) REVERT: A 636 ARG cc_start: 0.6867 (mmt180) cc_final: 0.6570 (mmm-85) REVERT: A 683 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6332 (tpt) REVERT: A 698 GLU cc_start: 0.7513 (tt0) cc_final: 0.6891 (tt0) REVERT: A 851 LYS cc_start: 0.6588 (tttp) cc_final: 0.6260 (tptt) outliers start: 29 outliers final: 10 residues processed: 96 average time/residue: 0.6139 time to fit residues: 62.8270 Evaluate side-chains 91 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.250787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.218259 restraints weight = 9506.517| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 1.99 r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9149 Z= 0.156 Angle : 0.585 8.793 13019 Z= 0.327 Chirality : 0.036 0.172 1504 Planarity : 0.005 0.080 1162 Dihedral : 21.978 100.366 2844 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 5.33 % Allowed : 15.45 % Favored : 79.22 % 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: -1.28 (0.32), residues: 713 helix: 0.22 (0.28), residues: 327 sheet: -1.20 (0.50), residues: 99 loop : -1.94 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 227 TYR 0.015 0.002 TYR A 241 PHE 0.018 0.002 PHE A 717 TRP 0.017 0.002 TRP A 520 HIS 0.008 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 9149) covalent geometry : angle 0.58500 / 0.33 (13019) hydrogen bonds : bond 0.04694 / 4.87 ( 392) hydrogen bonds : angle 4.63673 / 6.39 ( 1024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.339 Fit side-chains REVERT: A 90 LYS cc_start: 0.6605 (ptpt) cc_final: 0.6153 (pptt) REVERT: A 133 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6557 (mtt) REVERT: A 149 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6694 (pt0) REVERT: A 153 LYS cc_start: 0.8074 (tmmt) cc_final: 0.7740 (ttpp) REVERT: A 255 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6944 (pt0) REVERT: A 333 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7509 (mm) REVERT: A 340 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.5267 (tttm) REVERT: A 390 LYS cc_start: 0.6408 (mmtt) cc_final: 0.6181 (tppt) REVERT: A 410 GLN cc_start: 0.6782 (OUTLIER) cc_final: 0.6223 (tt0) REVERT: A 489 LYS cc_start: 0.7653 (ptpp) cc_final: 0.7273 (pttp) REVERT: A 572 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6633 (tp30) REVERT: A 698 GLU cc_start: 0.7256 (tt0) cc_final: 0.6731 (tt0) REVERT: A 851 LYS cc_start: 0.6780 (tttp) cc_final: 0.6500 (tptt) outliers start: 30 outliers final: 10 residues processed: 92 average time/residue: 0.6158 time to fit residues: 60.5461 Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 66 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 0.4980 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.252100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.219107 restraints weight = 9573.839| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 2.02 r_work: 0.4019 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9149 Z= 0.138 Angle : 0.573 7.110 13019 Z= 0.322 Chirality : 0.035 0.172 1504 Planarity : 0.005 0.092 1162 Dihedral : 21.969 100.032 2844 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.91 % Allowed : 18.47 % Favored : 77.62 % 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: -1.20 (0.32), residues: 713 helix: 0.32 (0.29), residues: 327 sheet: -1.15 (0.49), residues: 107 loop : -1.94 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 687 TYR 0.028 0.002 TYR A 197 PHE 0.012 0.001 PHE A 717 TRP 0.014 0.002 TRP A 520 HIS 0.005 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 ( 9149) covalent geometry : angle 0.57324 / 0.32 (13019) hydrogen bonds : bond 0.04507 / 4.70 ( 392) hydrogen bonds : angle 4.54774 / 6.32 ( 1024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.369 Fit side-chains REVERT: A 90 LYS cc_start: 0.6797 (ptpt) cc_final: 0.5702 (mmtm) REVERT: A 92 SER cc_start: 0.6794 (p) cc_final: 0.6455 (p) REVERT: A 133 MET cc_start: 0.7332 (OUTLIER) cc_final: 0.6953 (mtt) REVERT: A 149 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6562 (pt0) REVERT: A 197 TYR cc_start: 0.6358 (t80) cc_final: 0.6139 (t80) REVERT: A 333 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7542 (mm) REVERT: A 390 LYS cc_start: 0.6469 (mmtt) cc_final: 0.5979 (tppt) REVERT: A 410 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.6353 (tt0) REVERT: A 489 LYS cc_start: 0.7977 (ptpp) cc_final: 0.7564 (pttp) REVERT: A 572 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6244 (tp30) REVERT: A 636 ARG cc_start: 0.6854 (mmt180) cc_final: 0.6583 (mmm-85) REVERT: A 698 GLU cc_start: 0.7458 (tt0) cc_final: 0.6809 (tt0) REVERT: A 851 LYS cc_start: 0.6688 (tttp) cc_final: 0.6379 (tptt) REVERT: A 855 ARG cc_start: 0.4945 (tmm160) cc_final: 0.4614 (tpp-160) outliers start: 22 outliers final: 7 residues processed: 90 average time/residue: 0.5887 time to fit residues: 56.4391 Evaluate side-chains 85 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 82 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 451 GLN A 715 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.252059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.220947 restraints weight = 9582.375| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 1.87 r_work: 0.4046 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9149 Z= 0.145 Angle : 0.577 9.105 13019 Z= 0.320 Chirality : 0.035 0.166 1504 Planarity : 0.005 0.081 1162 Dihedral : 21.905 99.792 2844 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.02 % Allowed : 20.25 % Favored : 76.73 % 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: -1.13 (0.32), residues: 713 helix: 0.37 (0.29), residues: 327 sheet: -1.18 (0.48), residues: 113 loop : -1.88 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 687 TYR 0.020 0.002 TYR A 197 PHE 0.016 0.001 PHE A 717 TRP 0.015 0.002 TRP A 520 HIS 0.007 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 ( 9149) covalent geometry : angle 0.57669 / 0.32 (13019) hydrogen bonds : bond 0.04528 / 4.72 ( 392) hydrogen bonds : angle 4.59652 / 6.37 ( 1024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.224 Fit side-chains REVERT: A 26 LYS cc_start: 0.6626 (mmmt) cc_final: 0.6215 (mttt) REVERT: A 90 LYS cc_start: 0.6768 (ptpt) cc_final: 0.5732 (mmtm) REVERT: A 133 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6850 (mtt) REVERT: A 149 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6539 (pt0) REVERT: A 197 TYR cc_start: 0.6506 (t80) cc_final: 0.6241 (t80) REVERT: A 333 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7564 (mm) REVERT: A 334 ARG cc_start: 0.5569 (mmt90) cc_final: 0.4826 (mpt-90) REVERT: A 390 LYS cc_start: 0.6583 (mmtt) cc_final: 0.6098 (tppt) REVERT: A 410 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6404 (tt0) REVERT: A 489 LYS cc_start: 0.7998 (ptpp) cc_final: 0.7607 (pttp) REVERT: A 500 LYS cc_start: 0.7225 (mtpp) cc_final: 0.7017 (pmtt) REVERT: A 572 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6337 (tp30) REVERT: A 647 THR cc_start: 0.6985 (m) cc_final: 0.6668 (m) REVERT: A 698 GLU cc_start: 0.7401 (tt0) cc_final: 0.6701 (tt0) REVERT: A 851 LYS cc_start: 0.6890 (tttp) cc_final: 0.6574 (tptt) REVERT: A 855 ARG cc_start: 0.5355 (tmm160) cc_final: 0.5057 (tpp-160) outliers start: 17 outliers final: 7 residues processed: 84 average time/residue: 0.5794 time to fit residues: 51.9042 Evaluate side-chains 83 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN A 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.250527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.218328 restraints weight = 9476.438| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 1.94 r_work: 0.4014 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9149 Z= 0.161 Angle : 0.593 8.401 13019 Z= 0.325 Chirality : 0.036 0.166 1504 Planarity : 0.005 0.086 1162 Dihedral : 21.890 99.633 2844 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 3.37 % Allowed : 20.07 % Favored : 76.55 % 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: -1.22 (0.32), residues: 713 helix: 0.30 (0.29), residues: 327 sheet: -1.19 (0.48), residues: 113 loop : -1.96 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 687 TYR 0.019 0.002 TYR A 197 PHE 0.018 0.002 PHE A 717 TRP 0.019 0.002 TRP A 520 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 9149) covalent geometry : angle 0.59262 / 0.33 (13019) hydrogen bonds : bond 0.04618 / 4.80 ( 392) hydrogen bonds : angle 4.61564 / 6.33 ( 1024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.259 Fit side-chains REVERT: A 26 LYS cc_start: 0.6555 (mmmt) cc_final: 0.6178 (mttt) REVERT: A 90 LYS cc_start: 0.6590 (ptpt) cc_final: 0.5455 (mmtp) REVERT: A 133 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6881 (mtt) REVERT: A 149 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6489 (pt0) REVERT: A 333 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7539 (mm) REVERT: A 334 ARG cc_start: 0.5387 (mmt90) cc_final: 0.4874 (mpt-90) REVERT: A 390 LYS cc_start: 0.6722 (mmtt) cc_final: 0.6223 (tppt) REVERT: A 410 GLN cc_start: 0.7178 (OUTLIER) cc_final: 0.6573 (tt0) REVERT: A 489 LYS cc_start: 0.7899 (ptpp) cc_final: 0.7500 (pttp) REVERT: A 572 GLU cc_start: 0.7414 (mm-30) cc_final: 0.6374 (tp30) REVERT: A 647 THR cc_start: 0.7138 (m) cc_final: 0.6830 (m) REVERT: A 698 GLU cc_start: 0.7484 (tt0) cc_final: 0.7050 (tt0) REVERT: A 851 LYS cc_start: 0.6967 (tttp) cc_final: 0.6676 (tptt) outliers start: 19 outliers final: 8 residues processed: 85 average time/residue: 0.5864 time to fit residues: 53.2393 Evaluate side-chains 82 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 27 optimal weight: 6.9990 chunk 63 optimal weight: 0.0970 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.252208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.219770 restraints weight = 9483.638| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 2.00 r_work: 0.4027 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9149 Z= 0.138 Angle : 0.573 8.256 13019 Z= 0.319 Chirality : 0.035 0.175 1504 Planarity : 0.005 0.077 1162 Dihedral : 21.887 99.163 2844 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.02 % Allowed : 21.31 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.32), residues: 713 helix: 0.41 (0.29), residues: 327 sheet: -1.36 (0.51), residues: 101 loop : -1.94 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 687 TYR 0.017 0.002 TYR A 197 PHE 0.011 0.001 PHE A 717 TRP 0.014 0.002 TRP A 520 HIS 0.006 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 ( 9149) covalent geometry : angle 0.57298 / 0.32 (13019) hydrogen bonds : bond 0.04479 / 4.65 ( 392) hydrogen bonds : angle 4.51560 / 6.24 ( 1024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.246 Fit side-chains REVERT: A 26 LYS cc_start: 0.6667 (mmmt) cc_final: 0.6244 (mttt) REVERT: A 90 LYS cc_start: 0.6653 (ptpt) cc_final: 0.5474 (mmtp) REVERT: A 132 ASN cc_start: 0.6399 (OUTLIER) cc_final: 0.6187 (m110) REVERT: A 133 MET cc_start: 0.7266 (OUTLIER) cc_final: 0.6878 (mtt) REVERT: A 333 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7473 (mm) REVERT: A 334 ARG cc_start: 0.5318 (mmt90) cc_final: 0.4685 (mpt-90) REVERT: A 390 LYS cc_start: 0.6637 (mmtt) cc_final: 0.6119 (tppt) REVERT: A 410 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6326 (tt0) REVERT: A 572 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6347 (tp30) REVERT: A 684 GLN cc_start: 0.7566 (mm-40) cc_final: 0.6557 (mp10) REVERT: A 687 ARG cc_start: 0.6924 (mtp-110) cc_final: 0.6636 (mtm-85) REVERT: A 698 GLU cc_start: 0.7465 (tt0) cc_final: 0.6774 (tt0) REVERT: A 851 LYS cc_start: 0.6906 (tttp) cc_final: 0.6601 (tptt) REVERT: A 855 ARG cc_start: 0.5389 (tmm160) cc_final: 0.5089 (tpp-160) outliers start: 17 outliers final: 6 residues processed: 81 average time/residue: 0.6035 time to fit residues: 52.2010 Evaluate side-chains 81 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 41 optimal weight: 0.3980 chunk 84 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 62 optimal weight: 0.7980 chunk 38 optimal weight: 0.0570 overall best weight: 0.2698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN A 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.255150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.223346 restraints weight = 9513.829| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 1.99 r_work: 0.4066 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9149 Z= 0.125 Angle : 0.559 7.868 13019 Z= 0.313 Chirality : 0.034 0.171 1504 Planarity : 0.005 0.078 1162 Dihedral : 21.886 98.416 2844 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 1.78 % Allowed : 22.56 % Favored : 75.67 % 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: -1.09 (0.32), residues: 713 helix: 0.53 (0.29), residues: 327 sheet: -1.39 (0.51), residues: 100 loop : -1.94 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 687 TYR 0.017 0.002 TYR A 241 PHE 0.009 0.001 PHE A 453 TRP 0.016 0.002 TRP A 441 HIS 0.005 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 9149) covalent geometry : angle 0.55873 / 0.31 (13019) hydrogen bonds : bond 0.04205 / 4.42 ( 392) hydrogen bonds : angle 4.39021 / 6.11 ( 1024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1426 Ramachandran restraints generated. 713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.255 Fit side-chains REVERT: A 26 LYS cc_start: 0.6465 (mmmt) cc_final: 0.5989 (mttt) REVERT: A 90 LYS cc_start: 0.6710 (ptpt) cc_final: 0.5454 (mmtp) REVERT: A 133 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6973 (mtt) REVERT: A 333 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7395 (mm) REVERT: A 334 ARG cc_start: 0.5530 (mmt90) cc_final: 0.4969 (mpt-90) REVERT: A 390 LYS cc_start: 0.6398 (mmtt) cc_final: 0.5839 (tppt) REVERT: A 410 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6252 (tt0) REVERT: A 572 GLU cc_start: 0.7380 (mm-30) cc_final: 0.6154 (tp30) REVERT: A 684 GLN cc_start: 0.7375 (mm-40) cc_final: 0.6411 (mp10) REVERT: A 687 ARG cc_start: 0.6871 (mtp-110) cc_final: 0.6499 (mtm-85) REVERT: A 851 LYS cc_start: 0.6454 (tttp) cc_final: 0.6175 (tptt) REVERT: A 855 ARG cc_start: 0.4689 (tmm160) cc_final: 0.4438 (tpp-160) outliers start: 10 outliers final: 4 residues processed: 79 average time/residue: 0.5810 time to fit residues: 49.0008 Evaluate side-chains 81 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 0.0570 chunk 38 optimal weight: 0.0570 chunk 42 optimal weight: 0.0060 chunk 17 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 overall best weight: 0.3032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.255173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.222787 restraints weight = 9496.398| |-----------------------------------------------------------------------------| r_work (start): 0.4453 rms_B_bonded: 1.98 r_work: 0.4075 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 9149 Z= 0.124 Angle : 0.561 8.589 13019 Z= 0.311 Chirality : 0.034 0.166 1504 Planarity : 0.005 0.062 1162 Dihedral : 21.865 98.164 2844 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 1.78 % Allowed : 22.91 % Favored : 75.31 % 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: -1.03 (0.32), residues: 713 helix: 0.61 (0.29), residues: 327 sheet: -1.38 (0.51), residues: 100 loop : -1.94 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 687 TYR 0.017 0.001 TYR A 241 PHE 0.008 0.001 PHE A 717 TRP 0.013 0.002 TRP A 441 HIS 0.006 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 ( 9149) covalent geometry : angle 0.56056 / 0.31 (13019) hydrogen bonds : bond 0.04212 / 4.40 ( 392) hydrogen bonds : angle 4.34850 / 6.05 ( 1024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2677.94 seconds wall clock time: 46 minutes 34.09 seconds (2794.09 seconds total)