Starting phenix.real_space_refine on Wed Jan 15 16:04:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2i_38856/01_2025/8y2i_38856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2i_38856/01_2025/8y2i_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_38856/01_2025/8y2i_38856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2i_38856/01_2025/8y2i_38856.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2i_38856/01_2025/8y2i_38856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2i_38856/01_2025/8y2i_38856.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 3.14, per 1000 atoms: 0.36 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: 2.42 Conformation dependent library (CDL) restraints added in 731.0 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: 4.43 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: 4.90 Time building geometry restraints manager: 2.74 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: 12606 2.01 - 4.02: 341 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: 1444 0.098 - 0.196: 52 0.196 - 0.294: 5 0.294 - 0.392: 0 0.392 - 0.490: 3 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 2.47 2.05 0.42 2.00e-01 2.50e+01 4.49e+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 2.47 2.05 0.42 2.00e-01 2.50e+01 4.36e+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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.940 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 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= 0.372 Angle : 0.793 10.060 13019 Z= 0.494 Chirality : 0.047 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 PHE 0.036 0.002 PHE A 717 TYR 0.017 0.002 TYR A 241 ARG 0.012 0.001 ARG A 874 *********************** 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 : 0.703 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: 1.4803 time to fit residues: 168.9093 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 : 0.709 ------------------------------------------------------------------------------- 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 71 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.0670 chunk 77 optimal weight: 7.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.250242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.217183 restraints weight = 9417.983| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 2.03 r_work: 0.3997 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9149 Z= 0.244 Angle : 0.656 6.488 13019 Z= 0.341 Chirality : 0.037 0.171 1504 Planarity : 0.006 0.088 1162 Dihedral : 22.066 102.801 2845 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 3.20 % Allowed : 11.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.32), residues: 713 helix: -0.03 (0.29), residues: 320 sheet: -1.30 (0.49), residues: 104 loop : -2.12 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 520 HIS 0.006 0.001 HIS A 657 PHE 0.021 0.002 PHE A 717 TYR 0.019 0.002 TYR A 725 ARG 0.012 0.001 ARG A 855 *********************** 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: 18 poor density : 79 time to evaluate : 0.653 Fit side-chains REVERT: A 22 GLN cc_start: 0.7386 (mt0) cc_final: 0.7016 (mm110) REVERT: A 80 GLU cc_start: 0.6767 (tt0) cc_final: 0.6565 (tt0) REVERT: A 90 LYS cc_start: 0.6707 (ptpt) cc_final: 0.6296 (pptt) REVERT: A 133 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6992 (mtt) REVERT: A 155 TYR cc_start: 0.7539 (t80) cc_final: 0.6977 (t80) REVERT: A 262 TYR cc_start: 0.8071 (t80) cc_final: 0.7783 (t80) REVERT: A 384 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6521 (mt-10) REVERT: A 390 LYS cc_start: 0.6299 (mmtt) cc_final: 0.5572 (ptmm) REVERT: A 410 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6417 (tt0) REVERT: A 489 LYS cc_start: 0.7992 (ptpp) cc_final: 0.7673 (pttt) REVERT: A 636 ARG cc_start: 0.6832 (mmt180) cc_final: 0.6507 (mmm-85) REVERT: A 683 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6333 (tpt) REVERT: A 693 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7065 (mt-10) REVERT: A 698 GLU cc_start: 0.7455 (tt0) cc_final: 0.6851 (tt0) REVERT: A 850 ARG cc_start: 0.6079 (mtt-85) cc_final: 0.4890 (mtt-85) REVERT: A 851 LYS cc_start: 0.6649 (tttp) cc_final: 0.6349 (tptt) REVERT: A 855 ARG cc_start: 0.5417 (tpp-160) cc_final: 0.4665 (tmm160) outliers start: 18 outliers final: 5 residues processed: 86 average time/residue: 1.4398 time to fit residues: 131.0749 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 : 0.674 ------------------------------------------------------------------------------- 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 683 MET Chi-restraints excluded: chain A residue 704 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 81 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.0570 chunk 24 optimal weight: 0.1980 chunk 72 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 684 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.253698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.222524 restraints weight = 9563.047| |-----------------------------------------------------------------------------| r_work (start): 0.4459 rms_B_bonded: 1.92 r_work: 0.4075 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.2056 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= 0.176 Angle : 0.578 6.444 13019 Z= 0.304 Chirality : 0.034 0.174 1504 Planarity : 0.005 0.060 1162 Dihedral : 21.928 101.400 2844 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 3.55 % Allowed : 14.03 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.31), residues: 713 helix: 0.34 (0.28), residues: 329 sheet: -1.34 (0.48), residues: 98 loop : -1.95 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 441 HIS 0.006 0.001 HIS A 110 PHE 0.014 0.001 PHE A 717 TYR 0.017 0.002 TYR A 241 ARG 0.006 0.001 ARG A 687 *********************** 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 105 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.746 Fit side-chains REVERT: A 22 GLN cc_start: 0.7415 (mt0) cc_final: 0.7047 (mm110) REVERT: A 90 LYS cc_start: 0.6803 (ptpt) cc_final: 0.6287 (pptt) REVERT: A 133 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6615 (mtp) REVERT: A 153 LYS cc_start: 0.8013 (tmmt) cc_final: 0.7675 (ttpp) REVERT: A 262 TYR cc_start: 0.8011 (t80) cc_final: 0.7768 (t80) REVERT: A 303 GLN cc_start: 0.7856 (mt0) cc_final: 0.7621 (mt0) REVERT: A 390 LYS cc_start: 0.6277 (mmtt) cc_final: 0.5956 (tppt) REVERT: A 410 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6449 (tt0) REVERT: A 489 LYS cc_start: 0.7897 (ptpp) cc_final: 0.7498 (pttp) REVERT: A 636 ARG cc_start: 0.6848 (mmt180) cc_final: 0.6615 (mmm-85) REVERT: A 683 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6310 (tpt) REVERT: A 698 GLU cc_start: 0.7183 (tt0) cc_final: 0.6463 (tt0) REVERT: A 848 ILE cc_start: 0.5476 (OUTLIER) cc_final: 0.5194 (tt) REVERT: A 851 LYS cc_start: 0.6528 (tttp) cc_final: 0.6230 (tptt) outliers start: 20 outliers final: 3 residues processed: 95 average time/residue: 1.3765 time to fit residues: 138.5457 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 : 0.660 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 57 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 13 optimal weight: 0.0050 chunk 24 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** 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 = 0.4705 r_free = 0.4705 target = 0.252469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.220376 restraints weight = 9532.295| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 1.93 r_work: 0.4045 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.2277 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= 0.194 Angle : 0.594 6.802 13019 Z= 0.309 Chirality : 0.034 0.174 1504 Planarity : 0.005 0.086 1162 Dihedral : 21.872 101.207 2844 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.91 % Allowed : 14.39 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.32), residues: 713 helix: 0.42 (0.29), residues: 327 sheet: -1.18 (0.49), residues: 99 loop : -1.91 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 520 HIS 0.004 0.001 HIS A 657 PHE 0.018 0.001 PHE A 717 TYR 0.016 0.002 TYR A 241 ARG 0.013 0.001 ARG A 855 *********************** 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: 22 poor density : 81 time to evaluate : 0.678 Fit side-chains REVERT: A 22 GLN cc_start: 0.7449 (mt0) cc_final: 0.7085 (mm110) REVERT: A 80 GLU cc_start: 0.6915 (tt0) cc_final: 0.6699 (tt0) REVERT: A 90 LYS cc_start: 0.6761 (ptpt) cc_final: 0.6253 (pptt) REVERT: A 93 MET cc_start: 0.7275 (mtm) cc_final: 0.6927 (mtm) REVERT: A 133 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6673 (mtp) REVERT: A 153 LYS cc_start: 0.8004 (tmmt) cc_final: 0.7680 (ttpp) REVERT: A 262 TYR cc_start: 0.8005 (t80) cc_final: 0.7573 (t80) REVERT: A 303 GLN cc_start: 0.7887 (mt0) cc_final: 0.7641 (mt0) REVERT: A 384 GLU cc_start: 0.5825 (mt-10) cc_final: 0.5621 (tt0) REVERT: A 390 LYS cc_start: 0.6375 (mmtt) cc_final: 0.5947 (tppt) REVERT: A 410 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6314 (tt0) REVERT: A 489 LYS cc_start: 0.7960 (ptpp) cc_final: 0.7521 (pttp) REVERT: A 572 GLU cc_start: 0.7219 (mm-30) cc_final: 0.5895 (tp30) REVERT: A 636 ARG cc_start: 0.6870 (mmt180) cc_final: 0.6625 (mmm-85) REVERT: A 683 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6299 (tpt) REVERT: A 698 GLU cc_start: 0.7321 (tt0) cc_final: 0.6546 (tt0) REVERT: A 848 ILE cc_start: 0.5486 (OUTLIER) cc_final: 0.5222 (tt) REVERT: A 851 LYS cc_start: 0.6560 (tttp) cc_final: 0.6260 (tptt) REVERT: A 855 ARG cc_start: 0.5157 (tpp-160) cc_final: 0.4295 (tmm160) outliers start: 22 outliers final: 6 residues processed: 91 average time/residue: 1.3573 time to fit residues: 131.3626 Evaluate side-chains 83 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 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 683 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 261 GLN A 410 GLN ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.247440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.214633 restraints weight = 9353.077| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 1.94 r_work: 0.3962 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9149 Z= 0.310 Angle : 0.670 10.077 13019 Z= 0.344 Chirality : 0.038 0.165 1504 Planarity : 0.006 0.085 1162 Dihedral : 21.897 101.419 2844 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 4.80 % Allowed : 15.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.32), residues: 713 helix: 0.14 (0.29), residues: 327 sheet: -1.23 (0.48), residues: 109 loop : -2.02 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 520 HIS 0.006 0.001 HIS A 447 PHE 0.028 0.002 PHE A 717 TYR 0.016 0.002 TYR A 241 ARG 0.009 0.001 ARG A 687 *********************** 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 108 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7561 (mt0) cc_final: 0.7301 (mm110) REVERT: A 90 LYS cc_start: 0.6677 (ptpt) cc_final: 0.5722 (mmtm) REVERT: A 130 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7242 (mp) REVERT: A 133 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6830 (mtt) REVERT: A 149 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6623 (pt0) REVERT: A 153 LYS cc_start: 0.8180 (tmmt) cc_final: 0.7866 (ttpp) REVERT: A 255 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: A 262 TYR cc_start: 0.8116 (t80) cc_final: 0.7799 (t80) REVERT: A 303 GLN cc_start: 0.8028 (mt0) cc_final: 0.7814 (mt0) REVERT: A 333 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7546 (mm) REVERT: A 334 ARG cc_start: 0.5242 (mpt-90) cc_final: 0.5027 (mpt-90) REVERT: A 390 LYS cc_start: 0.6611 (mmtt) cc_final: 0.6123 (tppt) REVERT: A 410 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.6470 (tt0) REVERT: A 489 LYS cc_start: 0.8100 (ptpp) cc_final: 0.7718 (pttp) REVERT: A 500 LYS cc_start: 0.7327 (mtpp) cc_final: 0.6989 (pmmt) REVERT: A 572 GLU cc_start: 0.7510 (mm-30) cc_final: 0.6397 (OUTLIER) REVERT: A 683 MET cc_start: 0.6867 (OUTLIER) cc_final: 0.6528 (tpt) REVERT: A 850 ARG cc_start: 0.6499 (mtt-85) cc_final: 0.5543 (mtt-85) REVERT: A 851 LYS cc_start: 0.6967 (tttp) cc_final: 0.6697 (tptt) outliers start: 27 outliers final: 9 residues processed: 96 average time/residue: 1.3361 time to fit residues: 136.4814 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 : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 130 LEU 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 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 683 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 3 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 49 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 684 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 = 0.4693 r_free = 0.4693 target = 0.251408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.218881 restraints weight = 9362.991| |-----------------------------------------------------------------------------| r_work (start): 0.4415 rms_B_bonded: 1.95 r_work: 0.3994 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2576 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= 0.200 Angle : 0.599 8.475 13019 Z= 0.311 Chirality : 0.034 0.167 1504 Planarity : 0.005 0.090 1162 Dihedral : 21.894 100.537 2844 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 4.44 % Allowed : 17.58 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.32), residues: 713 helix: 0.38 (0.29), residues: 327 sheet: -1.18 (0.49), residues: 107 loop : -2.04 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 441 HIS 0.005 0.001 HIS A 14 PHE 0.014 0.001 PHE A 717 TYR 0.017 0.001 TYR A 241 ARG 0.011 0.000 ARG A 687 *********************** 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 101 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.747 Fit side-chains REVERT: A 22 GLN cc_start: 0.7465 (mt0) cc_final: 0.7077 (mm110) REVERT: A 90 LYS cc_start: 0.6817 (ptpt) cc_final: 0.5584 (mmtp) REVERT: A 133 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6925 (mtt) REVERT: A 149 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6543 (pt0) REVERT: A 153 LYS cc_start: 0.8038 (tmmt) cc_final: 0.7707 (ttpp) REVERT: A 255 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6998 (pt0) REVERT: A 262 TYR cc_start: 0.7992 (t80) cc_final: 0.7662 (t80) REVERT: A 303 GLN cc_start: 0.7883 (mt0) cc_final: 0.7628 (mt0) REVERT: A 333 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7439 (mm) REVERT: A 334 ARG cc_start: 0.5168 (mpt-90) cc_final: 0.4924 (mmt90) REVERT: A 390 LYS cc_start: 0.6426 (mmtt) cc_final: 0.5890 (tppt) REVERT: A 410 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6359 (tt0) REVERT: A 489 LYS cc_start: 0.8037 (ptpp) cc_final: 0.7639 (pttt) REVERT: A 500 LYS cc_start: 0.7225 (mtpp) cc_final: 0.6840 (pmmt) REVERT: A 572 GLU cc_start: 0.7410 (mm-30) cc_final: 0.6179 (OUTLIER) REVERT: A 683 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.6273 (tpt) REVERT: A 848 ILE cc_start: 0.5642 (OUTLIER) cc_final: 0.5378 (tt) REVERT: A 851 LYS cc_start: 0.6599 (tttp) cc_final: 0.6327 (tptt) outliers start: 25 outliers final: 11 residues processed: 88 average time/residue: 1.3402 time to fit residues: 125.7381 Evaluate side-chains 93 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 255 GLU 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 380 SER Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 53 optimal weight: 0.4980 chunk 40 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 0.0980 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.251679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.218546 restraints weight = 9511.433| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 1.96 r_work: 0.4030 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2709 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= 0.196 Angle : 0.600 8.013 13019 Z= 0.311 Chirality : 0.034 0.168 1504 Planarity : 0.005 0.084 1162 Dihedral : 21.875 100.311 2844 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 4.44 % Allowed : 19.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.32), residues: 713 helix: 0.50 (0.29), residues: 327 sheet: -1.17 (0.49), residues: 113 loop : -1.93 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 441 HIS 0.004 0.001 HIS A 14 PHE 0.014 0.001 PHE A 717 TYR 0.016 0.002 TYR A 241 ARG 0.012 0.000 ARG A 687 *********************** 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 102 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.712 Fit side-chains REVERT: A 22 GLN cc_start: 0.7470 (mt0) cc_final: 0.7132 (mm110) REVERT: A 90 LYS cc_start: 0.6783 (ptpt) cc_final: 0.5706 (mmtm) REVERT: A 133 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.6982 (mtt) REVERT: A 153 LYS cc_start: 0.8174 (tmmt) cc_final: 0.7825 (ttpp) REVERT: A 255 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7048 (pt0) REVERT: A 262 TYR cc_start: 0.8046 (t80) cc_final: 0.7786 (t80) REVERT: A 303 GLN cc_start: 0.7927 (mt0) cc_final: 0.7702 (mt0) REVERT: A 334 ARG cc_start: 0.5075 (mpt-90) cc_final: 0.4868 (mpt-90) REVERT: A 390 LYS cc_start: 0.6633 (mmtt) cc_final: 0.6100 (tppt) REVERT: A 410 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6406 (tt0) REVERT: A 489 LYS cc_start: 0.7949 (ptpp) cc_final: 0.7553 (pttt) REVERT: A 500 LYS cc_start: 0.7158 (mtpp) cc_final: 0.6850 (pmmt) REVERT: A 572 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6311 (OUTLIER) REVERT: A 683 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.6492 (tpt) REVERT: A 687 ARG cc_start: 0.6985 (mtp-110) cc_final: 0.5542 (ptm160) REVERT: A 848 ILE cc_start: 0.5936 (OUTLIER) cc_final: 0.5664 (tt) REVERT: A 851 LYS cc_start: 0.6818 (tttp) cc_final: 0.6533 (tptt) REVERT: A 855 ARG cc_start: 0.5956 (tpp-160) cc_final: 0.5709 (tpp-160) outliers start: 25 outliers final: 12 residues processed: 91 average time/residue: 1.3332 time to fit residues: 129.0354 Evaluate side-chains 89 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 190 THR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 260 GLU 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 455 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 27 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 0.0670 chunk 57 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 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 = 0.4699 r_free = 0.4699 target = 0.251938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.220063 restraints weight = 9517.437| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 1.87 r_work: 0.4027 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2847 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= 0.202 Angle : 0.600 9.071 13019 Z= 0.310 Chirality : 0.034 0.167 1504 Planarity : 0.005 0.084 1162 Dihedral : 21.865 99.915 2844 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.55 % Allowed : 20.43 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.32), residues: 713 helix: 0.59 (0.29), residues: 327 sheet: -1.14 (0.50), residues: 107 loop : -1.94 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 520 HIS 0.004 0.001 HIS A 110 PHE 0.014 0.001 PHE A 717 TYR 0.017 0.001 TYR A 241 ARG 0.010 0.000 ARG A 687 *********************** 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: 20 poor density : 76 time to evaluate : 0.674 Fit side-chains REVERT: A 22 GLN cc_start: 0.7404 (mt0) cc_final: 0.7093 (mm110) REVERT: A 90 LYS cc_start: 0.6714 (ptpt) cc_final: 0.5554 (mmtm) REVERT: A 133 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6930 (mtt) REVERT: A 153 LYS cc_start: 0.7969 (tmmt) cc_final: 0.7628 (ttpp) REVERT: A 255 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6907 (pt0) REVERT: A 262 TYR cc_start: 0.7986 (t80) cc_final: 0.7640 (t80) REVERT: A 303 GLN cc_start: 0.7943 (mt0) cc_final: 0.7689 (mt0) REVERT: A 332 VAL cc_start: 0.7256 (t) cc_final: 0.6967 (p) REVERT: A 410 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6447 (tt0) REVERT: A 500 LYS cc_start: 0.7203 (mtpp) cc_final: 0.6820 (pmmt) REVERT: A 572 GLU cc_start: 0.7346 (mm-30) cc_final: 0.6190 (OUTLIER) REVERT: A 636 ARG cc_start: 0.6841 (mmt180) cc_final: 0.6572 (mmm-85) REVERT: A 683 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6387 (tpt) REVERT: A 848 ILE cc_start: 0.5597 (OUTLIER) cc_final: 0.5326 (tt) REVERT: A 851 LYS cc_start: 0.6650 (tttp) cc_final: 0.6339 (tptt) REVERT: A 855 ARG cc_start: 0.5593 (tpp-160) cc_final: 0.5307 (tpp-160) outliers start: 20 outliers final: 12 residues processed: 86 average time/residue: 1.3093 time to fit residues: 119.8962 Evaluate side-chains 89 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 190 THR Chi-restraints excluded: chain A residue 255 GLU 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 455 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 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 = 0.4691 r_free = 0.4691 target = 0.250941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.217984 restraints weight = 9467.211| |-----------------------------------------------------------------------------| r_work (start): 0.4409 rms_B_bonded: 1.91 r_work: 0.3998 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9149 Z= 0.220 Angle : 0.612 8.280 13019 Z= 0.317 Chirality : 0.035 0.169 1504 Planarity : 0.005 0.076 1162 Dihedral : 21.864 99.725 2844 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 3.02 % Allowed : 21.85 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.32), residues: 713 helix: 0.53 (0.29), residues: 329 sheet: -1.12 (0.50), residues: 103 loop : -1.94 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 PHE 0.014 0.002 PHE A 717 TYR 0.016 0.001 TYR A 241 ARG 0.013 0.001 ARG A 687 *********************** 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 90 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.694 Fit side-chains REVERT: A 22 GLN cc_start: 0.7492 (mt0) cc_final: 0.7184 (mm110) REVERT: A 90 LYS cc_start: 0.6729 (ptpt) cc_final: 0.5578 (mmtm) REVERT: A 133 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6948 (mtt) REVERT: A 153 LYS cc_start: 0.7991 (tmmt) cc_final: 0.7655 (ttpp) REVERT: A 255 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6922 (pt0) REVERT: A 262 TYR cc_start: 0.7947 (t80) cc_final: 0.7669 (t80) REVERT: A 303 GLN cc_start: 0.7959 (mt0) cc_final: 0.7726 (mt0) REVERT: A 332 VAL cc_start: 0.7269 (t) cc_final: 0.7009 (p) REVERT: A 390 LYS cc_start: 0.6426 (mmtm) cc_final: 0.5488 (ptmm) REVERT: A 410 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6471 (tt0) REVERT: A 500 LYS cc_start: 0.7235 (mtpp) cc_final: 0.6856 (pmmt) REVERT: A 572 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6118 (tp30) REVERT: A 683 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6160 (tpt) REVERT: A 851 LYS cc_start: 0.6702 (tttp) cc_final: 0.6396 (tptt) REVERT: A 855 ARG cc_start: 0.5678 (tpp-160) cc_final: 0.5427 (tpp-160) outliers start: 17 outliers final: 11 residues processed: 81 average time/residue: 1.2574 time to fit residues: 108.7513 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 : 0.659 ------------------------------------------------------------------------------- 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 190 THR Chi-restraints excluded: chain A residue 255 GLU 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 455 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 683 MET 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 17 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 82 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.251355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.217819 restraints weight = 9490.302| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 1.96 r_work: 0.4008 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9149 Z= 0.214 Angle : 0.604 8.071 13019 Z= 0.312 Chirality : 0.035 0.168 1504 Planarity : 0.005 0.079 1162 Dihedral : 21.867 99.412 2844 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 3.20 % Allowed : 22.20 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.32), residues: 713 helix: 0.63 (0.29), residues: 326 sheet: -1.17 (0.50), residues: 103 loop : -1.97 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 520 HIS 0.004 0.001 HIS A 657 PHE 0.013 0.001 PHE A 717 TYR 0.018 0.001 TYR A 241 ARG 0.013 0.000 ARG A 687 ********************** 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 89 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.696 Fit side-chains REVERT: A 22 GLN cc_start: 0.7460 (mt0) cc_final: 0.7176 (mm110) REVERT: A 90 LYS cc_start: 0.6704 (ptpt) cc_final: 0.5587 (mmtm) REVERT: A 133 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6873 (mtt) REVERT: A 153 LYS cc_start: 0.8024 (tmmt) cc_final: 0.7667 (ttpp) REVERT: A 262 TYR cc_start: 0.8004 (t80) cc_final: 0.7752 (t80) REVERT: A 303 GLN cc_start: 0.7985 (mt0) cc_final: 0.7756 (mt0) REVERT: A 332 VAL cc_start: 0.7352 (t) cc_final: 0.7099 (p) REVERT: A 390 LYS cc_start: 0.6357 (mmtm) cc_final: 0.5383 (ptmm) REVERT: A 410 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6480 (tt0) REVERT: A 500 LYS cc_start: 0.7249 (mtpp) cc_final: 0.6890 (pmmt) REVERT: A 636 ARG cc_start: 0.6875 (mmt180) cc_final: 0.6553 (mmm-85) REVERT: A 683 MET cc_start: 0.6843 (OUTLIER) cc_final: 0.6227 (tpt) REVERT: A 851 LYS cc_start: 0.6751 (tttp) cc_final: 0.6444 (tptt) REVERT: A 855 ARG cc_start: 0.5760 (tpp-160) cc_final: 0.5514 (tpp-160) outliers start: 18 outliers final: 11 residues processed: 80 average time/residue: 1.3575 time to fit residues: 115.4975 Evaluate side-chains 86 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 190 THR 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 455 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 543 MET Chi-restraints excluded: chain A residue 683 MET 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 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 0.0000 chunk 58 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 80 optimal weight: 10.0000 overall best weight: 0.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.252963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.215521 restraints weight = 9450.362| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.13 r_work: 0.4023 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9149 Z= 0.183 Angle : 0.589 7.801 13019 Z= 0.306 Chirality : 0.034 0.169 1504 Planarity : 0.005 0.070 1162 Dihedral : 21.865 98.946 2844 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 2.49 % Allowed : 22.91 % Favored : 74.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.32), residues: 713 helix: 0.76 (0.29), residues: 326 sheet: -1.11 (0.51), residues: 103 loop : -1.94 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 441 HIS 0.004 0.001 HIS A 657 PHE 0.010 0.001 PHE A 717 TYR 0.018 0.001 TYR A 241 ARG 0.013 0.000 ARG A 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5285.58 seconds wall clock time: 94 minutes 38.85 seconds (5678.85 seconds total)