Starting phenix.real_space_refine on Thu Mar 13 03:24:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y2i_38856/03_2025/8y2i_38856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y2i_38856/03_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_38856/03_2025/8y2i_38856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y2i_38856/03_2025/8y2i_38856.map" model { file = "/net/cci-nas-00/data/ceres_data/8y2i_38856/03_2025/8y2i_38856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y2i_38856/03_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-5624/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: 5.28, per 1000 atoms: 0.61 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: 2.19 Conformation dependent library (CDL) restraints added in 620.2 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: 3.53 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: 4.58 Time building geometry restraints manager: 2.51 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: 1.050 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 26.370 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.280 ------------------------------------------------------------------------------- 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 : 0.831 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: 1.4553 time to fit residues: 166.4071 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 : 0.696 ------------------------------------------------------------------------------- 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 = 0.250240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.217047 restraints weight = 9417.891| |-----------------------------------------------------------------------------| r_work (start): 0.4407 rms_B_bonded: 2.04 r_work: 0.4002 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.1572 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 : 0.733 Fit side-chains REVERT: A 22 GLN cc_start: 0.7381 (mt0) cc_final: 0.7013 (mm110) REVERT: A 80 GLU cc_start: 0.6734 (tt0) cc_final: 0.6533 (tt0) REVERT: A 90 LYS cc_start: 0.6716 (ptpt) cc_final: 0.6290 (pptt) REVERT: A 133 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6984 (mtt) REVERT: A 155 TYR cc_start: 0.7548 (t80) cc_final: 0.6992 (t80) REVERT: A 262 TYR cc_start: 0.8093 (t80) cc_final: 0.7817 (t80) REVERT: A 384 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6534 (mt-10) REVERT: A 390 LYS cc_start: 0.6341 (mmtt) cc_final: 0.5638 (ptmm) REVERT: A 410 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6423 (tt0) REVERT: A 489 LYS cc_start: 0.8000 (ptpp) cc_final: 0.7681 (pttt) REVERT: A 636 ARG cc_start: 0.6868 (mmt180) cc_final: 0.6558 (mmm-85) REVERT: A 683 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6352 (tpt) REVERT: A 693 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7061 (mt-10) REVERT: A 698 GLU cc_start: 0.7450 (tt0) cc_final: 0.6841 (tt0) REVERT: A 850 ARG cc_start: 0.6114 (mtt-85) cc_final: 0.4939 (mtt-85) REVERT: A 851 LYS cc_start: 0.6697 (tttp) cc_final: 0.6389 (tptt) REVERT: A 855 ARG cc_start: 0.5470 (tpp-160) cc_final: 0.4744 (tmm160) outliers start: 18 outliers final: 5 residues processed: 86 average time/residue: 1.3540 time to fit residues: 123.4909 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 : 0.635 ------------------------------------------------------------------------------- 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: 0.4980 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 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 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 = 0.4696 r_free = 0.4696 target = 0.251281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.219897 restraints weight = 9535.123| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 1.87 r_work: 0.4048 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.1931 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 : 0.597 6.366 13019 Z= 0.312 Chirality : 0.035 0.174 1504 Planarity : 0.005 0.060 1162 Dihedral : 21.928 101.625 2844 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.09 % Allowed : 13.50 % 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: -1.33 (0.31), residues: 713 helix: 0.23 (0.29), residues: 328 sheet: -1.34 (0.48), residues: 98 loop : -1.99 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 520 HIS 0.005 0.001 HIS A 110 PHE 0.018 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 109 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.630 Fit side-chains REVERT: A 22 GLN cc_start: 0.7453 (mt0) cc_final: 0.7073 (mm110) REVERT: A 26 LYS cc_start: 0.6622 (mmmt) cc_final: 0.6212 (mttt) REVERT: A 80 GLU cc_start: 0.6954 (tt0) cc_final: 0.6734 (tt0) REVERT: A 90 LYS cc_start: 0.6765 (ptpt) cc_final: 0.6272 (pptt) REVERT: A 133 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6915 (mtt) REVERT: A 153 LYS cc_start: 0.7986 (tmmt) cc_final: 0.7653 (ttpp) REVERT: A 262 TYR cc_start: 0.7939 (t80) cc_final: 0.7666 (t80) REVERT: A 303 GLN cc_start: 0.7864 (mt0) cc_final: 0.7624 (mt0) REVERT: A 384 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6600 (mt-10) REVERT: A 390 LYS cc_start: 0.6301 (mmtt) cc_final: 0.5899 (tppt) REVERT: A 410 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6402 (tt0) REVERT: A 489 LYS cc_start: 0.7972 (ptpp) cc_final: 0.7561 (pttp) REVERT: A 572 GLU cc_start: 0.7263 (mm-30) cc_final: 0.5935 (tp30) REVERT: A 636 ARG cc_start: 0.6861 (mmt180) cc_final: 0.6598 (mmm-85) REVERT: A 683 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6344 (tpt) REVERT: A 698 GLU cc_start: 0.7386 (tt0) cc_final: 0.6792 (tt0) REVERT: A 848 ILE cc_start: 0.5534 (OUTLIER) cc_final: 0.5273 (tt) REVERT: A 851 LYS cc_start: 0.6513 (tttp) cc_final: 0.6193 (tptt) outliers start: 23 outliers final: 5 residues processed: 98 average time/residue: 1.3347 time to fit residues: 138.6988 Evaluate side-chains 83 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 52 optimal weight: 0.9980 chunk 25 optimal weight: 0.0050 chunk 84 optimal weight: 3.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4707 r_free = 0.4707 target = 0.252752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.220952 restraints weight = 9542.058| |-----------------------------------------------------------------------------| r_work (start): 0.4443 rms_B_bonded: 1.93 r_work: 0.4056 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2250 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= 0.188 Angle : 0.596 6.394 13019 Z= 0.310 Chirality : 0.034 0.175 1504 Planarity : 0.005 0.087 1162 Dihedral : 21.882 101.293 2844 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.37 % Allowed : 15.45 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.14 (0.32), residues: 713 helix: 0.39 (0.29), residues: 327 sheet: -1.16 (0.49), residues: 99 loop : -1.93 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 520 HIS 0.004 0.001 HIS A 110 PHE 0.017 0.001 PHE A 717 TYR 0.016 0.002 TYR A 241 ARG 0.010 0.000 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 100 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.655 Fit side-chains REVERT: A 22 GLN cc_start: 0.7463 (mt0) cc_final: 0.7063 (mm110) REVERT: A 80 GLU cc_start: 0.6932 (tt0) cc_final: 0.6710 (tt0) REVERT: A 90 LYS cc_start: 0.6775 (ptpt) cc_final: 0.6264 (pptt) REVERT: A 133 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6958 (mtt) REVERT: A 153 LYS cc_start: 0.8074 (tmmt) cc_final: 0.7749 (ttpp) REVERT: A 262 TYR cc_start: 0.8009 (t80) cc_final: 0.7707 (t80) REVERT: A 303 GLN cc_start: 0.7859 (mt0) cc_final: 0.7610 (mt0) REVERT: A 390 LYS cc_start: 0.6379 (mmtt) cc_final: 0.5940 (tppt) REVERT: A 410 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.6295 (tt0) REVERT: A 489 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7525 (pttp) REVERT: A 572 GLU cc_start: 0.7215 (mm-30) cc_final: 0.5899 (tp30) REVERT: A 636 ARG cc_start: 0.6870 (mmt180) cc_final: 0.6613 (mmm-85) REVERT: A 683 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.6293 (tpt) REVERT: A 698 GLU cc_start: 0.7365 (tt0) cc_final: 0.6637 (tt0) REVERT: A 851 LYS cc_start: 0.6560 (tttp) cc_final: 0.6256 (tptt) REVERT: A 855 ARG cc_start: 0.5080 (tpp-160) cc_final: 0.4844 (tpp-160) outliers start: 19 outliers final: 7 residues processed: 88 average time/residue: 1.2659 time to fit residues: 118.5777 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 : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 272 VAL 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 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: 0.0470 chunk 84 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- 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 = 0.4686 r_free = 0.4686 target = 0.250207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.217007 restraints weight = 9380.168| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 1.95 r_work: 0.4011 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9149 Z= 0.240 Angle : 0.610 7.253 13019 Z= 0.317 Chirality : 0.035 0.174 1504 Planarity : 0.005 0.086 1162 Dihedral : 21.863 101.139 2844 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.97 % Allowed : 15.45 % Favored : 79.57 % 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: -1.21 (0.32), residues: 713 helix: 0.34 (0.29), residues: 327 sheet: -1.14 (0.49), residues: 107 loop : -2.00 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 520 HIS 0.006 0.001 HIS A 14 PHE 0.021 0.002 PHE A 717 TYR 0.016 0.002 TYR A 241 ARG 0.010 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 106 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.670 Fit side-chains REVERT: A 22 GLN cc_start: 0.7448 (mt0) cc_final: 0.7176 (mm110) REVERT: A 90 LYS cc_start: 0.6604 (ptpt) cc_final: 0.5732 (mmtm) REVERT: A 130 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7171 (mp) REVERT: A 133 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6974 (mtt) REVERT: A 149 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6697 (pt0) REVERT: A 153 LYS cc_start: 0.8243 (tmmt) cc_final: 0.7914 (ttpp) REVERT: A 255 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7269 (pt0) REVERT: A 262 TYR cc_start: 0.8088 (t80) cc_final: 0.7794 (t80) REVERT: A 333 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7573 (mm) REVERT: A 334 ARG cc_start: 0.5942 (mmt90) cc_final: 0.5201 (mpt-90) REVERT: A 390 LYS cc_start: 0.6660 (mmtt) cc_final: 0.6211 (tppt) REVERT: A 410 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6524 (tt0) REVERT: A 489 LYS cc_start: 0.7922 (ptpp) cc_final: 0.7554 (pttp) REVERT: A 500 LYS cc_start: 0.7282 (mtpp) cc_final: 0.6991 (pmmt) REVERT: A 572 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6396 (tp30) REVERT: A 683 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6543 (tpt) REVERT: A 698 GLU cc_start: 0.7509 (tt0) cc_final: 0.6886 (tt0) REVERT: A 851 LYS cc_start: 0.6938 (tttp) cc_final: 0.6660 (tptt) outliers start: 28 outliers final: 10 residues processed: 93 average time/residue: 1.3303 time to fit residues: 132.0878 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 : 0.727 ------------------------------------------------------------------------------- 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 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 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 683 MET 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 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.0060 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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 = 0.4698 r_free = 0.4698 target = 0.251853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.219245 restraints weight = 9346.730| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 1.95 r_work: 0.3997 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2560 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= 0.204 Angle : 0.593 8.600 13019 Z= 0.308 Chirality : 0.034 0.165 1504 Planarity : 0.005 0.089 1162 Dihedral : 21.862 100.566 2844 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.59 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: -1.13 (0.32), residues: 713 helix: 0.41 (0.29), residues: 327 sheet: -1.05 (0.50), residues: 107 loop : -2.00 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 520 HIS 0.006 0.001 HIS A 14 PHE 0.018 0.001 PHE A 717 TYR 0.017 0.001 TYR A 241 ARG 0.013 0.001 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 102 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.666 Fit side-chains REVERT: A 22 GLN cc_start: 0.7521 (mt0) cc_final: 0.7161 (mm110) REVERT: A 48 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7398 (mp) REVERT: A 90 LYS cc_start: 0.6764 (ptpt) cc_final: 0.5689 (mmtm) REVERT: A 133 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.6947 (mtt) REVERT: A 149 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6520 (pt0) REVERT: A 255 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6864 (pt0) REVERT: A 262 TYR cc_start: 0.7972 (t80) cc_final: 0.7656 (t80) REVERT: A 333 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7490 (mm) REVERT: A 334 ARG cc_start: 0.5752 (mmt90) cc_final: 0.5168 (mpt-90) REVERT: A 390 LYS cc_start: 0.6549 (mmtt) cc_final: 0.6032 (tppt) REVERT: A 410 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6328 (tt0) REVERT: A 489 LYS cc_start: 0.8013 (ptpp) cc_final: 0.7606 (pttp) REVERT: A 500 LYS cc_start: 0.7276 (mtpp) cc_final: 0.6905 (pmmt) REVERT: A 572 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6248 (tp30) REVERT: A 683 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6366 (tpt) REVERT: A 698 GLU cc_start: 0.7494 (tt0) cc_final: 0.6852 (tt0) REVERT: A 848 ILE cc_start: 0.5769 (OUTLIER) cc_final: 0.5482 (tt) REVERT: A 851 LYS cc_start: 0.6798 (tttp) cc_final: 0.6516 (tptt) outliers start: 25 outliers final: 9 residues processed: 90 average time/residue: 1.3333 time to fit residues: 127.7235 Evaluate side-chains 85 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 48 ILE Chi-restraints excluded: chain A residue 133 MET Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 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 683 MET Chi-restraints excluded: chain A residue 733 CYS 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: 0.6980 chunk 40 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4695 r_free = 0.4695 target = 0.251433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.218896 restraints weight = 9498.780| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 1.91 r_work: 0.4052 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2654 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= 0.214 Angle : 0.603 8.706 13019 Z= 0.313 Chirality : 0.034 0.168 1504 Planarity : 0.005 0.082 1162 Dihedral : 21.857 100.343 2844 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % 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 (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: -1.08 (0.32), residues: 713 helix: 0.45 (0.29), residues: 327 sheet: -1.05 (0.50), residues: 108 loop : -1.97 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 520 HIS 0.005 0.001 HIS A 14 PHE 0.018 0.002 PHE A 717 TYR 0.016 0.001 TYR A 241 ARG 0.013 0.001 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 97 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.632 Fit side-chains REVERT: A 22 GLN cc_start: 0.7462 (mt0) cc_final: 0.7173 (mm110) REVERT: A 90 LYS cc_start: 0.6689 (ptpt) cc_final: 0.5654 (mmtm) REVERT: A 133 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6916 (mtt) REVERT: A 149 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6567 (pt0) REVERT: A 255 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7165 (pt0) REVERT: A 262 TYR cc_start: 0.8073 (t80) cc_final: 0.7830 (t80) REVERT: A 390 LYS cc_start: 0.6688 (mmtt) cc_final: 0.6207 (tppt) REVERT: A 410 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6366 (tt0) REVERT: A 489 LYS cc_start: 0.7924 (ptpp) cc_final: 0.7515 (pttp) REVERT: A 572 GLU cc_start: 0.7423 (mm-30) cc_final: 0.6430 (OUTLIER) REVERT: A 683 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6533 (tpt) REVERT: A 698 GLU cc_start: 0.7415 (tt0) cc_final: 0.6768 (tt0) REVERT: A 848 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5729 (tt) REVERT: A 851 LYS cc_start: 0.6913 (tttp) cc_final: 0.6640 (tptt) outliers start: 23 outliers final: 9 residues processed: 86 average time/residue: 1.2274 time to fit residues: 112.6152 Evaluate side-chains 84 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 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 501 THR Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 733 CYS 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: 4.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6142 ------------------------------------------------------------------------------- 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 = 0.4707 r_free = 0.4707 target = 0.252784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.220526 restraints weight = 9514.292| |-----------------------------------------------------------------------------| r_work (start): 0.4429 rms_B_bonded: 1.92 r_work: 0.4030 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2823 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= 0.193 Angle : 0.588 8.158 13019 Z= 0.306 Chirality : 0.034 0.167 1504 Planarity : 0.005 0.081 1162 Dihedral : 21.850 99.705 2844 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.20 % Allowed : 20.25 % 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 (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: -1.03 (0.32), residues: 713 helix: 0.52 (0.29), residues: 327 sheet: -1.09 (0.50), residues: 108 loop : -1.96 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 0.001 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 90 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7426 (mt0) cc_final: 0.7120 (mm110) REVERT: A 90 LYS cc_start: 0.6680 (ptpt) cc_final: 0.5577 (mmtm) REVERT: A 133 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6974 (mtt) REVERT: A 255 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6879 (pt0) REVERT: A 262 TYR cc_start: 0.8026 (t80) cc_final: 0.7755 (t80) REVERT: A 390 LYS cc_start: 0.6653 (mmtt) cc_final: 0.6225 (tppt) REVERT: A 410 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6350 (tt0) REVERT: A 572 GLU cc_start: 0.7356 (mm-30) cc_final: 0.6179 (OUTLIER) REVERT: A 636 ARG cc_start: 0.6871 (mmt180) cc_final: 0.6623 (mmm-85) REVERT: A 683 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6230 (tpt) REVERT: A 698 GLU cc_start: 0.7391 (tt0) cc_final: 0.6749 (tt0) REVERT: A 848 ILE cc_start: 0.5735 (OUTLIER) cc_final: 0.5450 (tt) REVERT: A 851 LYS cc_start: 0.6693 (tttp) cc_final: 0.6412 (tptt) outliers start: 18 outliers final: 8 residues processed: 81 average time/residue: 1.2650 time to fit residues: 109.2242 Evaluate side-chains 79 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 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 533 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 733 CYS 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: 0.8980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.2980 chunk 8 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 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 34 GLN A 214 GLN ** A 451 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 = 0.4707 r_free = 0.4707 target = 0.252805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.220302 restraints weight = 9476.282| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 1.91 r_work: 0.4027 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.2972 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= 0.191 Angle : 0.589 8.028 13019 Z= 0.305 Chirality : 0.034 0.167 1504 Planarity : 0.005 0.073 1162 Dihedral : 21.837 99.355 2844 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 2.66 % Allowed : 21.49 % Favored : 75.84 % 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: -0.96 (0.32), residues: 713 helix: 0.67 (0.29), residues: 324 sheet: -1.00 (0.52), residues: 102 loop : -2.03 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 520 HIS 0.004 0.001 HIS A 110 PHE 0.012 0.001 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 87 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.638 Fit side-chains REVERT: A 22 GLN cc_start: 0.7469 (mt0) cc_final: 0.7149 (mm110) REVERT: A 26 LYS cc_start: 0.6822 (mmmt) cc_final: 0.6434 (mttt) REVERT: A 90 LYS cc_start: 0.6650 (ptpt) cc_final: 0.5555 (mmtm) REVERT: A 133 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6991 (mtt) REVERT: A 255 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7013 (pt0) REVERT: A 262 TYR cc_start: 0.8075 (t80) cc_final: 0.7848 (t80) REVERT: A 390 LYS cc_start: 0.6743 (mmtt) cc_final: 0.6348 (tppt) REVERT: A 410 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6395 (tt0) REVERT: A 572 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6237 (tp30) REVERT: A 636 ARG cc_start: 0.6931 (mmt180) cc_final: 0.6705 (mmm-85) REVERT: A 683 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6253 (tpt) REVERT: A 698 GLU cc_start: 0.7373 (tt0) cc_final: 0.6700 (tt0) REVERT: A 848 ILE cc_start: 0.5809 (OUTLIER) cc_final: 0.5526 (tt) REVERT: A 851 LYS cc_start: 0.6775 (tttp) cc_final: 0.6477 (tptt) REVERT: A 855 ARG cc_start: 0.5809 (tpp-160) cc_final: 0.5497 (tpp-160) outliers start: 15 outliers final: 8 residues processed: 81 average time/residue: 1.1893 time to fit residues: 103.1028 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 : 0.701 ------------------------------------------------------------------------------- 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 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 533 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 701 LEU Chi-restraints excluded: chain A residue 733 CYS Chi-restraints excluded: chain A residue 848 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 17 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 67 optimal weight: 0.0970 chunk 82 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4708 r_free = 0.4708 target = 0.252970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.220418 restraints weight = 9489.781| |-----------------------------------------------------------------------------| r_work (start): 0.4428 rms_B_bonded: 1.95 r_work: 0.4015 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9149 Z= 0.193 Angle : 0.586 8.031 13019 Z= 0.305 Chirality : 0.034 0.167 1504 Planarity : 0.005 0.077 1162 Dihedral : 21.835 99.061 2844 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 2.66 % Allowed : 21.85 % Favored : 75.49 % 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: -0.92 (0.32), residues: 713 helix: 0.67 (0.29), residues: 326 sheet: -0.97 (0.51), residues: 102 loop : -1.99 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 PHE 0.013 0.001 PHE A 717 TYR 0.017 0.001 TYR A 241 ARG 0.013 0.001 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 84 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.636 Fit side-chains REVERT: A 22 GLN cc_start: 0.7447 (mt0) cc_final: 0.7103 (mm110) REVERT: A 26 LYS cc_start: 0.6630 (mmmt) cc_final: 0.6193 (mttt) REVERT: A 90 LYS cc_start: 0.6687 (ptpt) cc_final: 0.5543 (mmtm) REVERT: A 133 MET cc_start: 0.7308 (OUTLIER) cc_final: 0.6975 (mtt) REVERT: A 255 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.7025 (pt0) REVERT: A 262 TYR cc_start: 0.7899 (t80) cc_final: 0.7632 (t80) REVERT: A 390 LYS cc_start: 0.6595 (mmtt) cc_final: 0.6142 (tppt) REVERT: A 410 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6462 (tt0) REVERT: A 572 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6133 (tp30) REVERT: A 636 ARG cc_start: 0.6860 (mmt180) cc_final: 0.6586 (mmm-85) REVERT: A 683 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6171 (tpt) REVERT: A 698 GLU cc_start: 0.7411 (tt0) cc_final: 0.6758 (tt0) REVERT: A 851 LYS cc_start: 0.6650 (tttp) cc_final: 0.6352 (tptt) REVERT: A 855 ARG cc_start: 0.5595 (tpp-160) cc_final: 0.5266 (tpp-160) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 1.2468 time to fit residues: 102.5831 Evaluate side-chains 81 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 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 533 VAL Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 701 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 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.0980 chunk 60 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4713 r_free = 0.4713 target = 0.253634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.213316 restraints weight = 9456.162| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.21 r_work: 0.4017 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3113 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= 0.174 Angle : 0.579 8.043 13019 Z= 0.302 Chirality : 0.033 0.167 1504 Planarity : 0.005 0.069 1162 Dihedral : 21.834 99.001 2844 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 2.13 % Allowed : 22.38 % Favored : 75.49 % 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: -0.87 (0.32), residues: 713 helix: 0.71 (0.29), residues: 326 sheet: -0.98 (0.51), residues: 102 loop : -1.95 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 520 HIS 0.004 0.001 HIS A 14 PHE 0.011 0.001 PHE A 717 TYR 0.017 0.001 TYR A 241 ARG 0.014 0.001 ARG A 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5274.08 seconds wall clock time: 91 minutes 10.22 seconds (5470.22 seconds total)