Starting phenix.real_space_refine on Thu Jul 2 11:42:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2i_38856/07_2026/8y2i_38856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2i_38856/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y2i_38856/07_2026/8y2i_38856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2i_38856/07_2026/8y2i_38856.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2i_38856/07_2026/8y2i_38856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2i_38856/07_2026/8y2i_38856.cif" } 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-dev-6108/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: 1.77, per 1000 atoms: 0.20 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: 0.88 Conformation dependent library (CDL) restraints added in 214.7 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: 0.82 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: 1.72 Time building geometry restraints manager: 1.09 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 1.50e-02 4.44e+03 1.55e+01 bond pdb=" C LYS A 356 " pdb=" N LEU A 357 " ideal model delta sigma weight residual 1.334 1.279 0.056 1.43e-02 4.89e+03 1.51e+01 ... (remaining 9144 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 12558 2.01 - 4.02: 389 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=" 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 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 1.00e+00 1.00e+00 3.20e+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: 1418 0.098 - 0.196: 77 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: 1.130 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.720 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.990 ------------------------------------------------------------------------------- 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= 0.436 Angle : 0.818 10.060 13019 Z= 0.599 Chirality : 0.051 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 0.00594 / 0.44 ( 9149) covalent geometry : angle 0.81801 / 0.60 (13019) hydrogen bonds : bond 0.12353 / 14.09 ( 392) hydrogen bonds : angle 6.36460 / 8.74 ( 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 : 0.242 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 262 TYR cc_start: 0.8103 (t80) cc_final: 0.7790 (t80) REVERT: A 384 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6363 (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: 0.5682 (tt0) REVERT: A 693 GLU cc_start: 0.7223 (mt-10) cc_final: 0.7013 (mt-10) REVERT: A 850 ARG cc_start: 0.6083 (mtt-85) cc_final: 0.4648 (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: 0.6494 time to fit residues: 73.9250 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 : 0.237 ------------------------------------------------------------------------------- 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: 0.8980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 303 GLN ** A 684 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.250011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.217888 restraints weight = 9560.176| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 1.98 r_work: 0.3990 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9149 Z= 0.173 Angle : 0.633 7.032 13019 Z= 0.357 Chirality : 0.039 0.184 1504 Planarity : 0.006 0.091 1162 Dihedral : 22.161 104.266 2845 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 2.84 % Allowed : 11.55 % Favored : 85.61 % 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: -1.68 (0.31), residues: 713 helix: -0.06 (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 0.014 0.001 ARG A 855 TYR 0.020 0.002 TYR A 725 PHE 0.017 0.002 PHE A 717 TRP 0.016 0.002 TRP A 520 HIS 0.008 0.001 HIS A 657 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 9149) covalent geometry : angle 0.63261 / 0.36 (13019) hydrogen bonds : bond 0.05215 / 5.48 ( 392) hydrogen bonds : angle 5.02577 / 6.92 ( 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 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.161 Fit side-chains REVERT: A 22 GLN cc_start: 0.7466 (mt0) cc_final: 0.7166 (mm110) REVERT: A 90 LYS cc_start: 0.6750 (ptpt) cc_final: 0.6274 (pptt) REVERT: A 133 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.7001 (mtt) REVERT: A 155 TYR cc_start: 0.7607 (t80) cc_final: 0.7170 (t80) REVERT: A 197 TYR cc_start: 0.6677 (t80) cc_final: 0.6278 (t80) REVERT: A 262 TYR cc_start: 0.8114 (t80) cc_final: 0.7798 (t80) REVERT: A 384 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6530 (mt-10) REVERT: A 390 LYS cc_start: 0.6531 (mmtt) cc_final: 0.5781 (ptmm) REVERT: A 410 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6395 (tt0) REVERT: A 489 LYS cc_start: 0.7974 (ptpp) cc_final: 0.7693 (pttt) REVERT: A 636 ARG cc_start: 0.6854 (mmt180) cc_final: 0.6573 (mmm-85) REVERT: A 683 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6272 (tpt) REVERT: A 693 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7038 (mt-10) REVERT: A 698 GLU cc_start: 0.7401 (tt0) cc_final: 0.6832 (tt0) REVERT: A 850 ARG cc_start: 0.6230 (mtt-85) cc_final: 0.5110 (mtt-85) REVERT: A 851 LYS cc_start: 0.6816 (tttp) cc_final: 0.6503 (tptt) REVERT: A 855 ARG cc_start: 0.5457 (tpp-160) cc_final: 0.4850 (tmm160) outliers start: 16 outliers final: 4 residues processed: 87 average time/residue: 0.6259 time to fit residues: 57.5878 Evaluate side-chains 79 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.150 ------------------------------------------------------------------------------- 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 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 683 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 303 GLN 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 = 0.250773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.218655 restraints weight = 9500.313| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 1.95 r_work: 0.4041 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.1740 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= 0.155 Angle : 0.581 6.297 13019 Z= 0.330 Chirality : 0.037 0.177 1504 Planarity : 0.005 0.060 1162 Dihedral : 22.091 102.817 2844 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.44 % Allowed : 12.79 % Favored : 82.77 % 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: -1.42 (0.31), residues: 713 helix: 0.10 (0.28), residues: 327 sheet: -1.29 (0.49), residues: 98 loop : -2.00 (0.38), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 687 TYR 0.016 0.002 TYR A 241 PHE 0.017 0.002 PHE A 717 TRP 0.016 0.002 TRP A 520 HIS 0.005 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 ( 9149) covalent geometry : angle 0.58077 / 0.33 (13019) hydrogen bonds : bond 0.04726 / 4.94 ( 392) hydrogen bonds : angle 4.76220 / 6.57 ( 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 107 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.237 Fit side-chains REVERT: A 22 GLN cc_start: 0.7400 (mt0) cc_final: 0.7034 (mm110) REVERT: A 80 GLU cc_start: 0.7030 (tt0) cc_final: 0.6804 (tt0) REVERT: A 90 LYS cc_start: 0.6737 (ptpt) cc_final: 0.6269 (pptt) REVERT: A 133 MET cc_start: 0.7273 (OUTLIER) cc_final: 0.6867 (mtt) REVERT: A 153 LYS cc_start: 0.7995 (tmmt) cc_final: 0.7661 (ttpp) REVERT: A 155 TYR cc_start: 0.7548 (t80) cc_final: 0.7229 (t80) REVERT: A 197 TYR cc_start: 0.6599 (t80) cc_final: 0.6242 (t80) REVERT: A 262 TYR cc_start: 0.8116 (t80) cc_final: 0.7776 (t80) REVERT: A 303 GLN cc_start: 0.7863 (mt0) cc_final: 0.7621 (mt0) REVERT: A 328 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6574 (mt) REVERT: A 369 LEU cc_start: 0.8118 (mt) cc_final: 0.7892 (mt) REVERT: A 384 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6616 (mt-10) REVERT: A 390 LYS cc_start: 0.6323 (mmtt) cc_final: 0.6001 (tppt) REVERT: A 410 GLN cc_start: 0.6893 (OUTLIER) cc_final: 0.6339 (tt0) REVERT: A 489 LYS cc_start: 0.7981 (ptpp) cc_final: 0.7576 (pttp) REVERT: A 636 ARG cc_start: 0.6872 (mmt180) cc_final: 0.6594 (mmm-85) REVERT: A 683 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6330 (tpt) REVERT: A 698 GLU cc_start: 0.7415 (tt0) cc_final: 0.6789 (tt0) REVERT: A 851 LYS cc_start: 0.6576 (tttp) cc_final: 0.6248 (tptt) REVERT: A 855 ARG cc_start: 0.5352 (tpp-160) cc_final: 0.4713 (tmm160) outliers start: 25 outliers final: 6 residues processed: 92 average time/residue: 0.6266 time to fit residues: 61.0714 Evaluate side-chains 86 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 230 LYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 328 ILE 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: 10.0000 chunk 48 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 HIS 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 = 0.251778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.219263 restraints weight = 9598.797| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.00 r_work: 0.4023 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2010 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= 0.148 Angle : 0.578 6.441 13019 Z= 0.326 Chirality : 0.036 0.175 1504 Planarity : 0.005 0.088 1162 Dihedral : 22.058 102.363 2844 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 4.09 % Allowed : 14.03 % Favored : 81.88 % 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: -1.25 (0.32), residues: 713 helix: 0.29 (0.29), residues: 327 sheet: -1.30 (0.49), residues: 99 loop : -1.93 (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 0.019 0.002 PHE A 717 TRP 0.015 0.002 TRP A 520 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 ( 9149) covalent geometry : angle 0.57823 / 0.33 (13019) hydrogen bonds : bond 0.04590 / 4.76 ( 392) hydrogen bonds : angle 4.65247 / 6.44 ( 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 103 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.241 Fit side-chains REVERT: A 22 GLN cc_start: 0.7445 (mt0) cc_final: 0.7087 (mm110) REVERT: A 80 GLU cc_start: 0.6993 (tt0) cc_final: 0.6772 (tt0) REVERT: A 90 LYS cc_start: 0.6748 (ptpt) cc_final: 0.6234 (pptt) REVERT: A 133 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6845 (mtt) REVERT: A 153 LYS cc_start: 0.8087 (tmmt) cc_final: 0.7776 (ttpp) REVERT: A 155 TYR cc_start: 0.7617 (t80) cc_final: 0.7316 (t80) REVERT: A 197 TYR cc_start: 0.6629 (t80) cc_final: 0.6330 (t80) REVERT: A 262 TYR cc_start: 0.8039 (t80) cc_final: 0.7599 (t80) REVERT: A 303 GLN cc_start: 0.7895 (mt0) cc_final: 0.7644 (mt0) REVERT: A 384 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6624 (mt-10) REVERT: A 390 LYS cc_start: 0.6359 (mmtt) cc_final: 0.5939 (tppt) REVERT: A 410 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6405 (tt0) REVERT: A 489 LYS cc_start: 0.8011 (ptpp) cc_final: 0.7600 (pttp) REVERT: A 636 ARG cc_start: 0.6882 (mmt180) cc_final: 0.6610 (mmm-85) REVERT: A 683 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.6397 (tpt) REVERT: A 698 GLU cc_start: 0.7449 (tt0) cc_final: 0.6790 (tt0) REVERT: A 851 LYS cc_start: 0.6653 (tttp) cc_final: 0.6326 (tptt) outliers start: 23 outliers final: 8 residues processed: 90 average time/residue: 0.6077 time to fit residues: 58.1027 Evaluate side-chains 84 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 230 LYS Chi-restraints excluded: chain A residue 272 VAL 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: 9.9990 chunk 75 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 684 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.250572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.217152 restraints weight = 9513.925| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 2.03 r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2182 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= 0.160 Angle : 0.581 7.883 13019 Z= 0.327 Chirality : 0.037 0.170 1504 Planarity : 0.005 0.078 1162 Dihedral : 22.020 101.908 2844 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 5.86 % Allowed : 14.21 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.32), residues: 713 helix: 0.22 (0.28), residues: 327 sheet: -1.17 (0.50), residues: 99 loop : -1.91 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 687 TYR 0.016 0.002 TYR A 241 PHE 0.022 0.002 PHE A 717 TRP 0.018 0.002 TRP A 520 HIS 0.004 0.001 HIS A 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 ( 9149) covalent geometry : angle 0.58114 / 0.33 (13019) hydrogen bonds : bond 0.04613 / 4.75 ( 392) hydrogen bonds : angle 4.65703 / 6.37 ( 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 113 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.217 Fit side-chains REVERT: A 90 LYS cc_start: 0.6619 (ptpt) cc_final: 0.5568 (mmtp) REVERT: A 133 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6528 (mtt) REVERT: A 149 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6696 (pt0) REVERT: A 153 LYS cc_start: 0.8084 (tmmt) cc_final: 0.7749 (ttpp) REVERT: A 255 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7063 (pt0) REVERT: A 333 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7493 (mm) REVERT: A 410 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6219 (tt0) REVERT: A 489 LYS cc_start: 0.7663 (ptpp) cc_final: 0.7286 (pttp) REVERT: A 572 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6640 (tp30) REVERT: A 698 GLU cc_start: 0.7278 (tt0) cc_final: 0.6776 (tt0) REVERT: A 851 LYS cc_start: 0.6792 (tttp) cc_final: 0.6500 (tptt) outliers start: 33 outliers final: 10 residues processed: 97 average time/residue: 0.6244 time to fit residues: 64.1904 Evaluate side-chains 87 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR 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 230 LYS 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 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 Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 9.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 0.0670 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 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 = 0.251920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.219518 restraints weight = 9588.759| |-----------------------------------------------------------------------------| r_work (start): 0.4422 rms_B_bonded: 2.01 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: 0.7128 moved from start: 0.2417 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= 0.144 Angle : 0.572 7.258 13019 Z= 0.322 Chirality : 0.036 0.172 1504 Planarity : 0.005 0.092 1162 Dihedral : 22.017 101.749 2844 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 4.44 % Allowed : 18.12 % Favored : 77.44 % 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: -1.17 (0.32), residues: 713 helix: 0.37 (0.29), residues: 327 sheet: -1.15 (0.49), residues: 107 loop : -1.96 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 687 TYR 0.026 0.002 TYR A 197 PHE 0.013 0.001 PHE A 717 TRP 0.015 0.002 TRP A 520 HIS 0.005 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 9149) covalent geometry : angle 0.57193 / 0.32 (13019) hydrogen bonds : bond 0.04447 / 4.59 ( 392) hydrogen bonds : angle 4.60484 / 6.35 ( 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 104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.257 Fit side-chains REVERT: A 90 LYS cc_start: 0.6716 (ptpt) cc_final: 0.5697 (mmtp) REVERT: A 133 MET cc_start: 0.7409 (OUTLIER) cc_final: 0.6988 (mtt) REVERT: A 149 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6617 (pt0) REVERT: A 153 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7871 (ttpp) REVERT: A 197 TYR cc_start: 0.6563 (t80) cc_final: 0.6343 (t80) REVERT: A 333 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7493 (mm) REVERT: A 390 LYS cc_start: 0.6711 (mmtm) cc_final: 0.5736 (ptmm) REVERT: A 410 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6487 (tt0) REVERT: A 489 LYS cc_start: 0.7921 (ptpp) cc_final: 0.7540 (pttp) REVERT: A 572 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6404 (tp30) REVERT: A 698 GLU cc_start: 0.7449 (tt0) cc_final: 0.6758 (tt0) REVERT: A 851 LYS cc_start: 0.6927 (tttp) cc_final: 0.6632 (tptt) REVERT: A 855 ARG cc_start: 0.5491 (tmm160) cc_final: 0.5045 (tpp-160) outliers start: 25 outliers final: 10 residues processed: 93 average time/residue: 0.6055 time to fit residues: 60.0728 Evaluate side-chains 87 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 133 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LYS 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 380 SER 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 733 CYS 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: 0.6980 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 82 optimal weight: 20.0000 chunk 41 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 715 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4696 r_free = 0.4696 target = 0.251538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.218559 restraints weight = 9600.897| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 2.05 r_work: 0.4013 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2487 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= 0.149 Angle : 0.576 8.798 13019 Z= 0.322 Chirality : 0.036 0.167 1504 Planarity : 0.005 0.083 1162 Dihedral : 21.986 101.478 2844 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 3.55 % Allowed : 19.54 % Favored : 76.91 % 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: -1.12 (0.32), residues: 713 helix: 0.41 (0.29), residues: 327 sheet: -1.19 (0.48), residues: 113 loop : -1.92 (0.39), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 266 TYR 0.020 0.002 TYR A 197 PHE 0.016 0.001 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 0.00303 / 0.15 ( 9149) covalent geometry : angle 0.57560 / 0.32 (13019) hydrogen bonds : bond 0.04451 / 4.60 ( 392) hydrogen bonds : angle 4.61773 / 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 94 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.252 Fit side-chains REVERT: A 90 LYS cc_start: 0.6740 (ptpt) cc_final: 0.5826 (mmtm) REVERT: A 133 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6931 (mtt) REVERT: A 149 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: A 153 LYS cc_start: 0.8196 (tmmt) cc_final: 0.7867 (ttpp) REVERT: A 333 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7538 (mm) REVERT: A 334 ARG cc_start: 0.5811 (mmt90) cc_final: 0.5199 (mpt-90) REVERT: A 390 LYS cc_start: 0.6624 (mmtm) cc_final: 0.5662 (ptmm) REVERT: A 410 GLN cc_start: 0.7145 (OUTLIER) cc_final: 0.6460 (tt0) REVERT: A 489 LYS cc_start: 0.7909 (ptpp) cc_final: 0.7498 (pttp) REVERT: A 500 LYS cc_start: 0.6834 (OUTLIER) cc_final: 0.6555 (mtpp) REVERT: A 572 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6358 (tp30) REVERT: A 698 GLU cc_start: 0.7493 (tt0) cc_final: 0.6818 (tt0) REVERT: A 851 LYS cc_start: 0.6952 (tttp) cc_final: 0.6640 (tptt) outliers start: 20 outliers final: 10 residues processed: 84 average time/residue: 0.5678 time to fit residues: 50.9050 Evaluate side-chains 84 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 133 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU 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 500 LYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 44 optimal weight: 0.0070 chunk 78 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 43 optimal weight: 0.4980 chunk 74 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.4705 r_free = 0.4705 target = 0.252470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.220835 restraints weight = 9502.905| |-----------------------------------------------------------------------------| r_work (start): 0.4440 rms_B_bonded: 1.95 r_work: 0.4039 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2605 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= 0.137 Angle : 0.565 8.239 13019 Z= 0.316 Chirality : 0.035 0.168 1504 Planarity : 0.005 0.086 1162 Dihedral : 21.935 101.167 2844 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 4.09 % Allowed : 19.01 % Favored : 76.91 % 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: 0.50 (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 0.013 0.000 ARG A 687 TYR 0.018 0.002 TYR A 197 PHE 0.012 0.001 PHE A 717 TRP 0.014 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 ( 9149) covalent geometry : angle 0.56535 / 0.32 (13019) hydrogen bonds : bond 0.04314 / 4.46 ( 392) hydrogen bonds : angle 4.53149 / 6.24 ( 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 96 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.198 Fit side-chains REVERT: A 26 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6269 (mmmt) REVERT: A 90 LYS cc_start: 0.6810 (ptpt) cc_final: 0.5705 (mmtm) REVERT: A 133 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.6966 (mtt) REVERT: A 149 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6457 (pt0) REVERT: A 153 LYS cc_start: 0.7941 (tmmt) cc_final: 0.7607 (ttpp) REVERT: A 333 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7525 (mm) REVERT: A 334 ARG cc_start: 0.5506 (mmt90) cc_final: 0.4744 (mpt-90) REVERT: A 390 LYS cc_start: 0.6358 (mmtm) cc_final: 0.5351 (ptmm) REVERT: A 410 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.6324 (tt0) REVERT: A 489 LYS cc_start: 0.7957 (ptpp) cc_final: 0.7523 (pttp) REVERT: A 500 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6489 (mtpp) REVERT: A 572 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6201 (tp30) REVERT: A 698 GLU cc_start: 0.7420 (tt0) cc_final: 0.6765 (tt0) REVERT: A 851 LYS cc_start: 0.6556 (tttp) cc_final: 0.6244 (tptt) REVERT: A 855 ARG cc_start: 0.4906 (tmm160) cc_final: 0.4582 (tpp-160) outliers start: 23 outliers final: 10 residues processed: 85 average time/residue: 0.5603 time to fit residues: 50.6866 Evaluate side-chains 85 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 26 LYS 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 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.251728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.219031 restraints weight = 9497.342| |-----------------------------------------------------------------------------| r_work (start): 0.4418 rms_B_bonded: 2.01 r_work: 0.4024 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2700 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= 0.148 Angle : 0.574 8.298 13019 Z= 0.320 Chirality : 0.036 0.167 1504 Planarity : 0.005 0.077 1162 Dihedral : 21.907 100.876 2844 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.73 % Allowed : 19.72 % 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: -1.02 (0.32), residues: 713 helix: 0.53 (0.29), residues: 327 sheet: -1.12 (0.49), residues: 109 loop : -1.92 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 687 TYR 0.016 0.002 TYR A 241 PHE 0.015 0.002 PHE A 717 TRP 0.016 0.002 TRP A 520 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 9149) covalent geometry : angle 0.57430 / 0.32 (13019) hydrogen bonds : bond 0.04367 / 4.50 ( 392) hydrogen bonds : angle 4.55149 / 6.22 ( 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 92 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.240 Fit side-chains REVERT: A 90 LYS cc_start: 0.6642 (ptpt) cc_final: 0.5566 (mmtm) REVERT: A 133 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6863 (mtt) REVERT: A 153 LYS cc_start: 0.8196 (tmmt) cc_final: 0.7868 (ttpp) REVERT: A 333 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7510 (mm) REVERT: A 334 ARG cc_start: 0.5688 (mmt90) cc_final: 0.5056 (mpt-90) REVERT: A 390 LYS cc_start: 0.6589 (mmtm) cc_final: 0.5623 (ptmm) REVERT: A 410 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6470 (tt0) REVERT: A 572 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6331 (OUTLIER) REVERT: A 698 GLU cc_start: 0.7448 (tt0) cc_final: 0.6768 (tt0) REVERT: A 851 LYS cc_start: 0.6869 (tttp) cc_final: 0.6572 (tptt) REVERT: A 855 ARG cc_start: 0.5299 (tmm160) cc_final: 0.5099 (tpp-160) outliers start: 21 outliers final: 11 residues processed: 83 average time/residue: 0.5551 time to fit residues: 49.0319 Evaluate side-chains 83 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.239 ------------------------------------------------------------------------------- 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 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU 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 533 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 733 CYS 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: 0.9980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4705 r_free = 0.4705 target = 0.252494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.220442 restraints weight = 9498.341| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 1.97 r_work: 0.4037 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2760 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= 0.140 Angle : 0.570 8.060 13019 Z= 0.317 Chirality : 0.035 0.168 1504 Planarity : 0.005 0.082 1162 Dihedral : 21.909 100.717 2844 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.84 % Allowed : 20.78 % Favored : 76.38 % 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: -1.01 (0.32), residues: 713 helix: 0.56 (0.29), residues: 327 sheet: -1.13 (0.49), residues: 109 loop : -1.95 (0.38), residues: 277 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 0.011 0.001 PHE A 717 TRP 0.015 0.002 TRP A 520 HIS 0.005 0.001 HIS A 447 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 9149) covalent geometry : angle 0.56999 / 0.32 (13019) hydrogen bonds : bond 0.04286 / 4.42 ( 392) hydrogen bonds : angle 4.50358 / 6.19 ( 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 86 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.244 Fit side-chains REVERT: A 90 LYS cc_start: 0.6621 (ptpt) cc_final: 0.5631 (mmtm) REVERT: A 132 ASN cc_start: 0.6394 (OUTLIER) cc_final: 0.6153 (m110) REVERT: A 133 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: A 153 LYS cc_start: 0.8202 (tmmt) cc_final: 0.7872 (ttpp) REVERT: A 333 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7487 (mm) REVERT: A 334 ARG cc_start: 0.5636 (mmt90) cc_final: 0.5092 (mpt-90) REVERT: A 390 LYS cc_start: 0.6602 (mmtm) cc_final: 0.5664 (ptmm) REVERT: A 410 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.6429 (tt0) REVERT: A 572 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6318 (OUTLIER) REVERT: A 684 GLN cc_start: 0.7615 (mm-40) cc_final: 0.6572 (mp10) REVERT: A 687 ARG cc_start: 0.6949 (mtp-110) cc_final: 0.6610 (mtm-85) REVERT: A 698 GLU cc_start: 0.7407 (tt0) cc_final: 0.6759 (tt0) REVERT: A 851 LYS cc_start: 0.6878 (tttp) cc_final: 0.6587 (tptt) outliers start: 16 outliers final: 10 residues processed: 81 average time/residue: 0.5668 time to fit residues: 48.7918 Evaluate side-chains 85 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 190 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 333 LEU 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 533 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 733 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 42 optimal weight: 0.0170 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.253384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.221832 restraints weight = 9478.579| |-----------------------------------------------------------------------------| r_work (start): 0.4451 rms_B_bonded: 1.93 r_work: 0.4071 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.2887 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= 0.131 Angle : 0.558 7.891 13019 Z= 0.313 Chirality : 0.035 0.168 1504 Planarity : 0.005 0.073 1162 Dihedral : 21.897 100.326 2844 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.13 % Allowed : 21.67 % Favored : 76.20 % 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: 713 helix: 0.61 (0.29), residues: 327 sheet: -1.14 (0.49), residues: 109 loop : -1.92 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 687 TYR 0.017 0.001 TYR A 241 PHE 0.010 0.001 PHE A 717 TRP 0.013 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 9149) covalent geometry : angle 0.55825 / 0.31 (13019) hydrogen bonds : bond 0.04172 / 4.33 ( 392) hydrogen bonds : angle 4.45394 / 6.15 ( 1024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2426.69 seconds wall clock time: 42 minutes 9.78 seconds (2529.78 seconds total)