Starting phenix.real_space_refine on Thu Mar 6 07:56:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdr_37143/03_2025/8kdr_37143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdr_37143/03_2025/8kdr_37143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kdr_37143/03_2025/8kdr_37143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdr_37143/03_2025/8kdr_37143.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdr_37143/03_2025/8kdr_37143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdr_37143/03_2025/8kdr_37143.cif" } resolution = 3.4 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= 0.001 sd= 0.015 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: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3455 2.51 5 N 925 2.21 5 O 1053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5454 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "H" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1639 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "A" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2184 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 18, 'TRANS': 257} Time building chain proxies: 4.53, per 1000 atoms: 0.83 Number of scatterers: 5454 At special positions: 0 Unit cell: (101.15, 94.01, 108.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1053 8.00 N 925 7.00 C 3455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 680.3 milliseconds 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 13 sheets defined 3.4% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.619A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.894A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS L 127 " --> pdb=" O ASP L 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.911A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.741A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.748A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 11 removed outlier: 5.951A pdb=" N HIS L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU L 46 " --> pdb=" O HIS L 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.560A pdb=" N PHE L 117 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU L 136 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 146 through 151 removed outlier: 3.724A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR L 198 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN L 148 " --> pdb=" O GLU L 196 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 150 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA L 194 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.590A pdb=" N ARG H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AA7, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.943A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 171 through 173 removed outlier: 4.008A pdb=" N VAL H 188 " --> pdb=" O HIS H 171 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER H 186 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.843A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.843A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.800A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.583A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 539 through 541 88 hydrogen bonds defined for protein. 210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 985 1.32 - 1.45: 1492 1.45 - 1.57: 3090 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5591 Sorted by residual: bond pdb=" CA SER H 184 " pdb=" CB SER H 184 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.35e-02 5.49e+03 2.07e+01 bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.78e+01 bond pdb=" N ILE H 119 " pdb=" CA ILE H 119 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" CA SER L 14 " pdb=" CB SER L 14 " ideal model delta sigma weight residual 1.535 1.468 0.067 1.93e-02 2.68e+03 1.20e+01 bond pdb=" CA SER L 7 " pdb=" CB SER L 7 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.62e-02 3.81e+03 1.10e+01 ... (remaining 5586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 6674 2.30 - 4.60: 831 4.60 - 6.90: 85 6.90 - 9.20: 14 9.20 - 11.50: 4 Bond angle restraints: 7608 Sorted by residual: angle pdb=" N LEU H 166 " pdb=" CA LEU H 166 " pdb=" C LEU H 166 " ideal model delta sigma weight residual 111.82 103.35 8.47 1.16e+00 7.43e-01 5.33e+01 angle pdb=" CA PHE A 541 " pdb=" CB PHE A 541 " pdb=" CG PHE A 541 " ideal model delta sigma weight residual 113.80 120.37 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" C THR L 53 " pdb=" CA THR L 53 " pdb=" CB THR L 53 " ideal model delta sigma weight residual 111.41 101.68 9.73 1.65e+00 3.67e-01 3.48e+01 angle pdb=" CA PHE A 565 " pdb=" CB PHE A 565 " pdb=" CG PHE A 565 " ideal model delta sigma weight residual 113.80 119.58 -5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" CA PHE A 374 " pdb=" CB PHE A 374 " pdb=" CG PHE A 374 " ideal model delta sigma weight residual 113.80 119.51 -5.71 1.00e+00 1.00e+00 3.26e+01 ... (remaining 7603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 2855 16.61 - 33.23: 246 33.23 - 49.84: 157 49.84 - 66.45: 74 66.45 - 83.06: 6 Dihedral angle restraints: 3338 sinusoidal: 1293 harmonic: 2045 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -155.84 69.84 1 1.00e+01 1.00e-02 6.29e+01 dihedral pdb=" C SER L 94 " pdb=" N SER L 94 " pdb=" CA SER L 94 " pdb=" CB SER L 94 " ideal model delta harmonic sigma weight residual -122.60 -139.88 17.28 0 2.50e+00 1.60e-01 4.78e+01 dihedral pdb=" N SER L 94 " pdb=" C SER L 94 " pdb=" CA SER L 94 " pdb=" CB SER L 94 " ideal model delta harmonic sigma weight residual 122.80 136.39 -13.59 0 2.50e+00 1.60e-01 2.95e+01 ... (remaining 3335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 685 0.125 - 0.251: 138 0.251 - 0.376: 18 0.376 - 0.501: 3 0.501 - 0.626: 1 Chirality restraints: 845 Sorted by residual: chirality pdb=" CA SER L 94 " pdb=" N SER L 94 " pdb=" C SER L 94 " pdb=" CB SER L 94 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.80e+00 chirality pdb=" CA PRO L 95 " pdb=" N PRO L 95 " pdb=" C PRO L 95 " pdb=" CB PRO L 95 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA PHE H 153 " pdb=" N PHE H 153 " pdb=" C PHE H 153 " pdb=" CB PHE H 153 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 842 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 58 " 0.021 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C VAL L 58 " -0.069 2.00e-02 2.50e+03 pdb=" O VAL L 58 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO L 59 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 370 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.76e+00 pdb=" C ASN A 370 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN A 370 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE A 371 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 61 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ARG L 61 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG L 61 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE L 62 " -0.013 2.00e-02 2.50e+03 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1603 2.81 - 3.33: 4610 3.33 - 3.85: 9274 3.85 - 4.38: 10677 4.38 - 4.90: 17516 Nonbonded interactions: 43680 Sorted by model distance: nonbonded pdb=" O SER A 366 " pdb=" ND2 ASN A 370 " model vdw 2.287 3.120 nonbonded pdb=" O SER A 408 " pdb=" NE2 GLN A 414 " model vdw 2.311 3.120 nonbonded pdb=" NE2 GLN L 148 " pdb=" O GLU L 196 " model vdw 2.338 3.120 nonbonded pdb=" OE1 GLU L 166 " pdb=" N GLN L 167 " model vdw 2.372 3.120 nonbonded pdb=" O PRO A 445 " pdb=" OG SER A 446 " model vdw 2.409 3.040 ... (remaining 43675 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: 3.580 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.030 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 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 : 0.010 0.067 5591 Z= 0.634 Angle : 1.488 11.501 7608 Z= 1.028 Chirality : 0.102 0.626 845 Planarity : 0.005 0.050 981 Dihedral : 18.676 83.063 2005 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 3.00 % Allowed : 17.14 % Favored : 79.86 % Rotamer: Outliers : 26.92 % Allowed : 11.91 % Favored : 61.17 % Cbeta Deviations : 1.23 % 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: -5.71 (0.24), residues: 700 helix: -4.45 (0.50), residues: 25 sheet: -3.34 (0.33), residues: 174 loop : -4.26 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 353 HIS 0.007 0.001 HIS H 35 PHE 0.035 0.003 PHE A 541 TYR 0.027 0.002 TYR H 152 ARG 0.006 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 179 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 5 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.7885 (p) REVERT: L 8 PRO cc_start: 0.8111 (OUTLIER) cc_final: 0.7871 (Cg_endo) REVERT: L 42 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7793 (mtpp) REVERT: L 63 SER cc_start: 0.7800 (OUTLIER) cc_final: 0.7250 (p) REVERT: L 85 THR cc_start: 0.7172 (OUTLIER) cc_final: 0.6879 (p) REVERT: L 103 THR cc_start: 0.8292 (p) cc_final: 0.8045 (m) REVERT: L 104 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7362 (ttpp) REVERT: L 110 THR cc_start: 0.7318 (OUTLIER) cc_final: 0.6892 (p) REVERT: L 124 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7219 (pm20) REVERT: L 177 SER cc_start: 0.7946 (t) cc_final: 0.7685 (p) REVERT: H 21 SER cc_start: 0.8170 (t) cc_final: 0.7912 (p) REVERT: H 57 THR cc_start: 0.8341 (OUTLIER) cc_final: 0.8138 (m) REVERT: H 59 TYR cc_start: 0.7830 (m-80) cc_final: 0.7249 (m-80) REVERT: H 64 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7915 (ttmm) REVERT: H 127 SER cc_start: 0.6470 (OUTLIER) cc_final: 0.6011 (t) REVERT: H 159 VAL cc_start: 0.7945 (OUTLIER) cc_final: 0.7712 (t) REVERT: H 212 THR cc_start: 0.6139 (OUTLIER) cc_final: 0.5658 (t) REVERT: A 336 CYS cc_start: 0.5383 (OUTLIER) cc_final: 0.5066 (m) REVERT: A 349 SER cc_start: 0.8555 (t) cc_final: 0.8174 (t) REVERT: A 364 ASP cc_start: 0.7097 (t0) cc_final: 0.6424 (t0) REVERT: A 365 TYR cc_start: 0.7690 (m-80) cc_final: 0.6965 (m-80) REVERT: A 371 PHE cc_start: 0.6736 (t80) cc_final: 0.6443 (t80) REVERT: A 374 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: A 382 VAL cc_start: 0.8151 (t) cc_final: 0.7781 (p) REVERT: A 402 ILE cc_start: 0.7142 (OUTLIER) cc_final: 0.6892 (pt) REVERT: A 406 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6932 (mm-30) REVERT: A 425 LEU cc_start: 0.8410 (mt) cc_final: 0.8116 (mp) REVERT: A 428 ASP cc_start: 0.6367 (t0) cc_final: 0.6153 (t0) REVERT: A 440 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7421 (mmmt) REVERT: A 442 ASP cc_start: 0.7272 (m-30) cc_final: 0.6857 (m-30) REVERT: A 444 LYS cc_start: 0.7353 (mptp) cc_final: 0.7070 (mptp) REVERT: A 472 ILE cc_start: 0.7312 (mm) cc_final: 0.6743 (tp) REVERT: A 511 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7571 (t) REVERT: A 513 LEU cc_start: 0.7761 (mt) cc_final: 0.7544 (mt) REVERT: A 515 PHE cc_start: 0.6851 (m-80) cc_final: 0.6190 (m-80) REVERT: A 527 PRO cc_start: 0.7996 (Cg_endo) cc_final: 0.7669 (Cg_exo) REVERT: A 563 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6983 (mt0) REVERT: A 581 THR cc_start: 0.6873 (OUTLIER) cc_final: 0.6196 (m) outliers start: 165 outliers final: 64 residues processed: 288 average time/residue: 0.2063 time to fit residues: 73.9876 Evaluate side-chains 252 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 168 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 8 PRO Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain L residue 124 GLU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 148 GLN Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 591 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.0060 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 overall best weight: 0.2312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN L 37 HIS L 89 GLN L 90 GLN L 101 GLN L 125 GLN L 148 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 207 HIS A 409 GLN A 414 GLN A 487 ASN A 544 ASN A 556 ASN A 563 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.186115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.165152 restraints weight = 9396.419| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.91 r_work: 0.3983 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5591 Z= 0.219 Angle : 0.735 8.281 7608 Z= 0.381 Chirality : 0.048 0.254 845 Planarity : 0.006 0.057 981 Dihedral : 14.576 88.186 942 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.29 % Favored : 87.29 % Rotamer: Outliers : 14.03 % Allowed : 19.58 % Favored : 66.39 % 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: -5.09 (0.26), residues: 700 helix: -4.01 (0.65), residues: 26 sheet: -3.20 (0.32), residues: 183 loop : -3.67 (0.24), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 97 HIS 0.016 0.002 HIS L 190 PHE 0.023 0.002 PHE A 429 TYR 0.018 0.002 TYR L 141 ARG 0.008 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 152 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 46 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8078 (mt) REVERT: L 63 SER cc_start: 0.7330 (OUTLIER) cc_final: 0.6982 (p) REVERT: L 85 THR cc_start: 0.7282 (OUTLIER) cc_final: 0.7007 (p) REVERT: L 99 PHE cc_start: 0.7973 (m-80) cc_final: 0.7635 (m-80) REVERT: L 177 SER cc_start: 0.8142 (t) cc_final: 0.7912 (p) REVERT: L 191 LYS cc_start: 0.6561 (mtmm) cc_final: 0.6058 (mtmm) REVERT: H 43 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6316 (mmmm) REVERT: H 54 SER cc_start: 0.7356 (OUTLIER) cc_final: 0.7140 (p) REVERT: H 59 TYR cc_start: 0.8105 (m-80) cc_final: 0.7835 (m-80) REVERT: H 68 THR cc_start: 0.7926 (OUTLIER) cc_final: 0.7689 (m) REVERT: H 83 ASN cc_start: 0.7000 (m-40) cc_final: 0.6701 (m-40) REVERT: H 107 TYR cc_start: 0.7312 (OUTLIER) cc_final: 0.6556 (m-80) REVERT: A 336 CYS cc_start: 0.5672 (OUTLIER) cc_final: 0.5195 (m) REVERT: A 350 VAL cc_start: 0.8167 (OUTLIER) cc_final: 0.7927 (t) REVERT: A 356 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7854 (tmtp) REVERT: A 365 TYR cc_start: 0.7882 (m-80) cc_final: 0.7375 (m-80) REVERT: A 371 PHE cc_start: 0.6267 (t80) cc_final: 0.6031 (t80) REVERT: A 402 ILE cc_start: 0.7549 (OUTLIER) cc_final: 0.7339 (pt) REVERT: A 418 ILE cc_start: 0.8576 (mm) cc_final: 0.8368 (mm) REVERT: A 428 ASP cc_start: 0.6838 (t0) cc_final: 0.6570 (t0) REVERT: A 440 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7474 (mmmt) REVERT: A 442 ASP cc_start: 0.7503 (m-30) cc_final: 0.7123 (m-30) REVERT: A 461 LEU cc_start: 0.7907 (tp) cc_final: 0.7564 (mp) REVERT: A 511 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7940 (t) REVERT: A 515 PHE cc_start: 0.7048 (m-80) cc_final: 0.6517 (m-80) REVERT: A 528 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6353 (mtmt) REVERT: A 576 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7869 (t) outliers start: 86 outliers final: 41 residues processed: 209 average time/residue: 0.2148 time to fit residues: 55.2873 Evaluate side-chains 194 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 138 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 12 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN L 89 GLN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.172427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.149033 restraints weight = 9115.447| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.19 r_work: 0.3786 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 5591 Z= 0.508 Angle : 0.910 10.199 7608 Z= 0.478 Chirality : 0.055 0.253 845 Planarity : 0.007 0.063 981 Dihedral : 11.506 59.469 848 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.57 % Allowed : 15.14 % Favored : 84.29 % Rotamer: Outliers : 11.75 % Allowed : 24.96 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.44 % 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: -4.78 (0.27), residues: 700 helix: -3.66 (0.73), residues: 32 sheet: -3.03 (0.31), residues: 199 loop : -3.41 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP H 47 HIS 0.014 0.003 HIS L 190 PHE 0.028 0.003 PHE L 83 TYR 0.025 0.003 TYR H 94 ARG 0.005 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 148 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 63 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7386 (p) REVERT: L 79 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6781 (pm20) REVERT: L 82 ASP cc_start: 0.6686 (m-30) cc_final: 0.6301 (m-30) REVERT: L 85 THR cc_start: 0.7773 (OUTLIER) cc_final: 0.7478 (t) REVERT: L 99 PHE cc_start: 0.8064 (m-80) cc_final: 0.7804 (m-80) REVERT: L 107 ILE cc_start: 0.6474 (OUTLIER) cc_final: 0.6226 (mm) REVERT: H 7 SER cc_start: 0.8584 (p) cc_final: 0.8360 (p) REVERT: H 43 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6486 (mmmm) REVERT: H 68 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8107 (m) REVERT: H 92 MET cc_start: 0.7988 (tpp) cc_final: 0.7590 (tpp) REVERT: H 107 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.7016 (m-80) REVERT: A 336 CYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5590 (m) REVERT: A 353 TRP cc_start: 0.8353 (p-90) cc_final: 0.8079 (p-90) REVERT: A 356 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7902 (tmtp) REVERT: A 364 ASP cc_start: 0.7507 (t0) cc_final: 0.7100 (t0) REVERT: A 365 TYR cc_start: 0.8152 (m-80) cc_final: 0.7935 (m-80) REVERT: A 382 VAL cc_start: 0.8308 (t) cc_final: 0.7945 (p) REVERT: A 386 LYS cc_start: 0.7994 (mttp) cc_final: 0.7708 (mttp) REVERT: A 425 LEU cc_start: 0.8631 (mt) cc_final: 0.8401 (mt) REVERT: A 428 ASP cc_start: 0.7161 (t0) cc_final: 0.6815 (t0) REVERT: A 440 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7664 (mmmt) REVERT: A 466 ARG cc_start: 0.7348 (tpp80) cc_final: 0.7103 (tpp80) REVERT: A 471 GLU cc_start: 0.7134 (pp20) cc_final: 0.6894 (pp20) REVERT: A 511 VAL cc_start: 0.8248 (OUTLIER) cc_final: 0.8038 (t) REVERT: A 515 PHE cc_start: 0.6992 (m-80) cc_final: 0.6781 (m-80) REVERT: A 535 LYS cc_start: 0.7950 (mtpp) cc_final: 0.7293 (mtpp) REVERT: A 536 ASN cc_start: 0.8114 (m-40) cc_final: 0.7803 (m110) REVERT: A 560 LEU cc_start: 0.9076 (mt) cc_final: 0.8856 (mm) REVERT: A 576 VAL cc_start: 0.8136 (OUTLIER) cc_final: 0.7876 (t) outliers start: 72 outliers final: 45 residues processed: 195 average time/residue: 0.2056 time to fit residues: 49.8360 Evaluate side-chains 193 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 136 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 0.1980 chunk 33 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS A 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.176333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152499 restraints weight = 9355.689| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 3.31 r_work: 0.3833 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 5591 Z= 0.265 Angle : 0.772 14.352 7608 Z= 0.393 Chirality : 0.049 0.297 845 Planarity : 0.006 0.065 981 Dihedral : 10.363 59.024 833 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.00 % Favored : 89.57 % Rotamer: Outliers : 10.44 % Allowed : 25.45 % Favored : 64.11 % 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: -4.44 (0.28), residues: 700 helix: -3.84 (0.66), residues: 38 sheet: -2.98 (0.31), residues: 205 loop : -3.00 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 97 HIS 0.014 0.002 HIS L 190 PHE 0.021 0.002 PHE A 371 TYR 0.016 0.002 TYR A 453 ARG 0.008 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 135 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 21 ILE cc_start: 0.8421 (mt) cc_final: 0.8189 (mm) REVERT: L 28 THR cc_start: 0.8417 (t) cc_final: 0.8208 (p) REVERT: L 85 THR cc_start: 0.7710 (m) cc_final: 0.7404 (p) REVERT: L 124 GLU cc_start: 0.7222 (pm20) cc_final: 0.6895 (pm20) REVERT: H 43 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6534 (mmmm) REVERT: H 68 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7929 (m) REVERT: H 92 MET cc_start: 0.8003 (tpp) cc_final: 0.7588 (tpp) REVERT: H 107 TYR cc_start: 0.7759 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: H 173 PHE cc_start: 0.7184 (m-10) cc_final: 0.6860 (m-10) REVERT: A 349 SER cc_start: 0.8581 (t) cc_final: 0.8310 (t) REVERT: A 350 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8050 (p) REVERT: A 353 TRP cc_start: 0.8354 (p-90) cc_final: 0.7943 (p-90) REVERT: A 355 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7786 (mmm160) REVERT: A 356 LYS cc_start: 0.8197 (tmtp) cc_final: 0.7750 (tmtp) REVERT: A 365 TYR cc_start: 0.8099 (m-80) cc_final: 0.7878 (m-80) REVERT: A 382 VAL cc_start: 0.8253 (t) cc_final: 0.7842 (p) REVERT: A 386 LYS cc_start: 0.7861 (mttp) cc_final: 0.7541 (mttp) REVERT: A 428 ASP cc_start: 0.6989 (t0) cc_final: 0.6651 (t0) REVERT: A 440 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7660 (mmmt) REVERT: A 471 GLU cc_start: 0.7137 (pp20) cc_final: 0.6842 (pp20) REVERT: A 515 PHE cc_start: 0.7006 (m-80) cc_final: 0.6759 (m-80) REVERT: A 535 LYS cc_start: 0.7652 (mtpp) cc_final: 0.7349 (ttmm) REVERT: A 556 ASN cc_start: 0.7741 (t0) cc_final: 0.7031 (t0) REVERT: A 558 LYS cc_start: 0.8396 (mptm) cc_final: 0.7885 (mptm) outliers start: 64 outliers final: 39 residues processed: 178 average time/residue: 0.2073 time to fit residues: 45.7525 Evaluate side-chains 182 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 138 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 0.1980 chunk 57 optimal weight: 0.0040 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.2730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.176520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.153219 restraints weight = 9399.148| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.25 r_work: 0.3854 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 5591 Z= 0.208 Angle : 0.706 11.041 7608 Z= 0.356 Chirality : 0.047 0.244 845 Planarity : 0.005 0.052 981 Dihedral : 9.118 59.126 823 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.43 % Favored : 89.14 % Rotamer: Outliers : 9.14 % Allowed : 25.94 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.15 (0.29), residues: 700 helix: -3.61 (0.80), residues: 32 sheet: -2.77 (0.31), residues: 227 loop : -2.78 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 97 HIS 0.004 0.001 HIS H 171 PHE 0.022 0.002 PHE A 371 TYR 0.018 0.001 TYR A 453 ARG 0.009 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: L 85 THR cc_start: 0.7570 (m) cc_final: 0.7327 (p) REVERT: L 124 GLU cc_start: 0.7258 (pm20) cc_final: 0.6901 (pm20) REVERT: L 155 LEU cc_start: 0.1031 (OUTLIER) cc_final: 0.0706 (mt) REVERT: H 13 GLN cc_start: 0.8758 (mt0) cc_final: 0.8553 (mt0) REVERT: H 43 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6375 (mmmm) REVERT: H 48 VAL cc_start: 0.4068 (OUTLIER) cc_final: 0.2861 (t) REVERT: H 68 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7897 (m) REVERT: H 92 MET cc_start: 0.7792 (tpp) cc_final: 0.7367 (tpp) REVERT: H 107 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.6555 (m-80) REVERT: H 173 PHE cc_start: 0.7209 (m-10) cc_final: 0.6818 (m-10) REVERT: A 353 TRP cc_start: 0.8315 (p-90) cc_final: 0.7950 (p-90) REVERT: A 355 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7618 (mmm160) REVERT: A 365 TYR cc_start: 0.8078 (m-80) cc_final: 0.7859 (m-80) REVERT: A 382 VAL cc_start: 0.8159 (t) cc_final: 0.7724 (p) REVERT: A 386 LYS cc_start: 0.7781 (mttp) cc_final: 0.7429 (mttp) REVERT: A 398 ASP cc_start: 0.7598 (m-30) cc_final: 0.7125 (m-30) REVERT: A 428 ASP cc_start: 0.7026 (t0) cc_final: 0.6748 (t0) REVERT: A 440 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7622 (mmmt) REVERT: A 471 GLU cc_start: 0.7177 (pp20) cc_final: 0.6883 (pp20) REVERT: A 515 PHE cc_start: 0.6997 (m-80) cc_final: 0.6785 (m-80) REVERT: A 535 LYS cc_start: 0.7650 (mtpp) cc_final: 0.7032 (mtpp) REVERT: A 536 ASN cc_start: 0.8222 (m-40) cc_final: 0.7940 (m110) REVERT: A 543 PHE cc_start: 0.7627 (m-80) cc_final: 0.7386 (m-80) REVERT: A 556 ASN cc_start: 0.7698 (t0) cc_final: 0.6963 (t0) REVERT: A 558 LYS cc_start: 0.8390 (mptm) cc_final: 0.7859 (mptm) outliers start: 56 outliers final: 37 residues processed: 176 average time/residue: 0.2126 time to fit residues: 46.9691 Evaluate side-chains 179 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 62 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 34 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 343 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.173546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.150025 restraints weight = 9257.526| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 3.27 r_work: 0.3807 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5591 Z= 0.301 Angle : 0.762 11.799 7608 Z= 0.385 Chirality : 0.049 0.251 845 Planarity : 0.006 0.057 981 Dihedral : 8.882 58.751 816 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.00 % Favored : 88.57 % Rotamer: Outliers : 9.30 % Allowed : 26.10 % Favored : 64.60 % 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: -4.05 (0.29), residues: 700 helix: -3.11 (0.99), residues: 26 sheet: -2.83 (0.31), residues: 221 loop : -2.70 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 436 HIS 0.005 0.001 HIS H 35 PHE 0.021 0.002 PHE A 371 TYR 0.017 0.002 TYR L 141 ARG 0.009 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 136 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 79 GLN cc_start: 0.7729 (pm20) cc_final: 0.7370 (pm20) REVERT: L 82 ASP cc_start: 0.6920 (m-30) cc_final: 0.6387 (m-30) REVERT: L 85 THR cc_start: 0.7696 (m) cc_final: 0.7410 (p) REVERT: H 43 LYS cc_start: 0.7020 (OUTLIER) cc_final: 0.6488 (mmmm) REVERT: H 48 VAL cc_start: 0.4330 (OUTLIER) cc_final: 0.3097 (t) REVERT: H 68 THR cc_start: 0.8225 (OUTLIER) cc_final: 0.8001 (m) REVERT: H 107 TYR cc_start: 0.7708 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: A 353 TRP cc_start: 0.8394 (p-90) cc_final: 0.8158 (p-90) REVERT: A 364 ASP cc_start: 0.7505 (t0) cc_final: 0.7228 (t0) REVERT: A 386 LYS cc_start: 0.7942 (mttp) cc_final: 0.7611 (mttp) REVERT: A 428 ASP cc_start: 0.6900 (t0) cc_final: 0.6588 (t0) REVERT: A 440 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7696 (mmmt) REVERT: A 466 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7333 (tpp80) REVERT: A 471 GLU cc_start: 0.7269 (pp20) cc_final: 0.6880 (pp20) REVERT: A 535 LYS cc_start: 0.7652 (mtpp) cc_final: 0.6973 (mtpp) REVERT: A 536 ASN cc_start: 0.8189 (m-40) cc_final: 0.7854 (m110) REVERT: A 543 PHE cc_start: 0.7826 (m-80) cc_final: 0.7485 (m-80) REVERT: A 556 ASN cc_start: 0.7719 (t0) cc_final: 0.6941 (t0) REVERT: A 558 LYS cc_start: 0.8439 (mptm) cc_final: 0.7868 (mptm) outliers start: 57 outliers final: 38 residues processed: 172 average time/residue: 0.2147 time to fit residues: 45.9986 Evaluate side-chains 185 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN A 360 ASN ** A 409 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 = 0.4174 r_free = 0.4174 target = 0.171542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.148399 restraints weight = 9093.932| |-----------------------------------------------------------------------------| r_work (start): 0.3887 rms_B_bonded: 3.20 r_work: 0.3763 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 5591 Z= 0.350 Angle : 0.781 11.736 7608 Z= 0.399 Chirality : 0.051 0.250 845 Planarity : 0.006 0.056 981 Dihedral : 9.043 59.970 815 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.00 % Favored : 87.71 % Rotamer: Outliers : 8.81 % Allowed : 26.43 % Favored : 64.76 % 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: -3.83 (0.29), residues: 700 helix: -2.41 (1.25), residues: 20 sheet: -2.53 (0.32), residues: 223 loop : -2.68 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 97 HIS 0.006 0.002 HIS H 35 PHE 0.018 0.002 PHE A 371 TYR 0.015 0.002 TYR L 141 ARG 0.010 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 135 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 28 THR cc_start: 0.8505 (t) cc_final: 0.8245 (p) REVERT: L 79 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7143 (pm20) REVERT: L 85 THR cc_start: 0.7740 (m) cc_final: 0.7417 (p) REVERT: L 155 LEU cc_start: 0.0929 (OUTLIER) cc_final: 0.0671 (mt) REVERT: H 43 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6547 (mmmm) REVERT: H 56 ASP cc_start: 0.7687 (OUTLIER) cc_final: 0.7058 (p0) REVERT: H 68 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.8006 (m) REVERT: H 107 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: A 355 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7797 (mmm160) REVERT: A 356 LYS cc_start: 0.8229 (tmtp) cc_final: 0.7862 (tmtp) REVERT: A 358 ILE cc_start: 0.7866 (mt) cc_final: 0.7629 (mt) REVERT: A 386 LYS cc_start: 0.7975 (mttp) cc_final: 0.7634 (mttp) REVERT: A 428 ASP cc_start: 0.6999 (t0) cc_final: 0.6675 (t0) REVERT: A 439 ASN cc_start: 0.7859 (t0) cc_final: 0.7578 (t0) REVERT: A 440 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7713 (mmmt) REVERT: A 471 GLU cc_start: 0.7219 (pp20) cc_final: 0.6829 (pp20) REVERT: A 535 LYS cc_start: 0.7659 (mtpp) cc_final: 0.7311 (mtpp) REVERT: A 543 PHE cc_start: 0.8101 (m-80) cc_final: 0.7605 (m-80) REVERT: A 556 ASN cc_start: 0.7693 (t0) cc_final: 0.6856 (t0) REVERT: A 558 LYS cc_start: 0.8445 (mptm) cc_final: 0.7847 (mptm) REVERT: A 573 THR cc_start: 0.7630 (m) cc_final: 0.7290 (p) REVERT: A 583 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6710 (tt0) outliers start: 54 outliers final: 41 residues processed: 170 average time/residue: 0.2059 time to fit residues: 43.4157 Evaluate side-chains 183 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.172096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.148917 restraints weight = 9076.716| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.21 r_work: 0.3782 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.5861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5591 Z= 0.315 Angle : 0.776 11.146 7608 Z= 0.391 Chirality : 0.050 0.247 845 Planarity : 0.006 0.055 981 Dihedral : 8.872 59.716 814 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.86 % Favored : 88.86 % Rotamer: Outliers : 8.16 % Allowed : 27.24 % Favored : 64.60 % 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: -3.75 (0.29), residues: 700 helix: -2.49 (1.20), residues: 20 sheet: -2.54 (0.32), residues: 222 loop : -2.57 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 97 HIS 0.005 0.001 HIS H 35 PHE 0.016 0.002 PHE A 515 TYR 0.012 0.002 TYR A 421 ARG 0.011 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 134 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7690 (m) cc_final: 0.7396 (p) REVERT: H 7 SER cc_start: 0.8370 (p) cc_final: 0.8169 (p) REVERT: H 43 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6595 (mmmm) REVERT: H 56 ASP cc_start: 0.7657 (p0) cc_final: 0.7417 (p0) REVERT: H 68 THR cc_start: 0.8227 (OUTLIER) cc_final: 0.8001 (m) REVERT: H 107 TYR cc_start: 0.7734 (OUTLIER) cc_final: 0.6590 (m-80) REVERT: A 347 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6370 (m-80) REVERT: A 355 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7690 (mmm160) REVERT: A 356 LYS cc_start: 0.8288 (tmtp) cc_final: 0.7887 (tmtp) REVERT: A 358 ILE cc_start: 0.7855 (mt) cc_final: 0.7594 (mt) REVERT: A 386 LYS cc_start: 0.7913 (mttp) cc_final: 0.7566 (mttp) REVERT: A 428 ASP cc_start: 0.6959 (t0) cc_final: 0.6640 (t0) REVERT: A 439 ASN cc_start: 0.7784 (t0) cc_final: 0.7569 (t0) REVERT: A 440 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7691 (mmmt) REVERT: A 471 GLU cc_start: 0.7212 (pp20) cc_final: 0.6778 (pp20) REVERT: A 535 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7382 (ttmm) REVERT: A 558 LYS cc_start: 0.8397 (mptm) cc_final: 0.7796 (mptm) REVERT: A 573 THR cc_start: 0.7654 (m) cc_final: 0.7319 (p) REVERT: A 583 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6681 (tt0) outliers start: 50 outliers final: 43 residues processed: 171 average time/residue: 0.2066 time to fit residues: 43.8821 Evaluate side-chains 183 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 134 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 42 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 343 ASN A 414 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.172898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.149782 restraints weight = 9164.849| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.22 r_work: 0.3801 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5591 Z= 0.264 Angle : 0.745 10.830 7608 Z= 0.375 Chirality : 0.048 0.234 845 Planarity : 0.006 0.058 981 Dihedral : 8.607 59.458 812 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.86 % Favored : 88.86 % Rotamer: Outliers : 7.67 % Allowed : 27.41 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.59 (0.30), residues: 700 helix: -3.14 (0.97), residues: 26 sheet: -2.43 (0.33), residues: 223 loop : -2.40 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 97 HIS 0.005 0.001 HIS H 35 PHE 0.020 0.002 PHE A 515 TYR 0.012 0.002 TYR A 423 ARG 0.013 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 143 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7673 (m) cc_final: 0.7392 (p) REVERT: H 43 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6559 (mmmm) REVERT: H 68 THR cc_start: 0.8196 (OUTLIER) cc_final: 0.7971 (m) REVERT: H 107 TYR cc_start: 0.7714 (OUTLIER) cc_final: 0.6660 (m-80) REVERT: A 355 ARG cc_start: 0.8006 (mmm160) cc_final: 0.7714 (mmm160) REVERT: A 356 LYS cc_start: 0.8276 (tmtp) cc_final: 0.7854 (tmtp) REVERT: A 386 LYS cc_start: 0.7831 (mttp) cc_final: 0.7467 (mttp) REVERT: A 428 ASP cc_start: 0.6928 (t0) cc_final: 0.6660 (t0) REVERT: A 439 ASN cc_start: 0.7787 (t0) cc_final: 0.7565 (t0) REVERT: A 440 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7663 (mmmt) REVERT: A 466 ARG cc_start: 0.7908 (tpp80) cc_final: 0.7643 (tpp80) REVERT: A 471 GLU cc_start: 0.7283 (pp20) cc_final: 0.6856 (pp20) REVERT: A 535 LYS cc_start: 0.7642 (mtpp) cc_final: 0.6959 (ttmm) REVERT: A 536 ASN cc_start: 0.8252 (m-40) cc_final: 0.7770 (m110) REVERT: A 553 THR cc_start: 0.8514 (t) cc_final: 0.8240 (p) REVERT: A 558 LYS cc_start: 0.8371 (mptm) cc_final: 0.7778 (mptm) REVERT: A 573 THR cc_start: 0.7652 (m) cc_final: 0.7326 (p) REVERT: A 583 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6707 (tt0) outliers start: 47 outliers final: 41 residues processed: 174 average time/residue: 0.2001 time to fit residues: 43.8752 Evaluate side-chains 186 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 140 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 44 optimal weight: 0.1980 chunk 20 optimal weight: 0.0270 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 28 optimal weight: 0.9980 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.175193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.152046 restraints weight = 9221.229| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 3.27 r_work: 0.3837 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5591 Z= 0.203 Angle : 0.723 10.480 7608 Z= 0.361 Chirality : 0.047 0.226 845 Planarity : 0.006 0.056 981 Dihedral : 8.303 59.877 810 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.29 % Favored : 91.43 % Rotamer: Outliers : 7.01 % Allowed : 28.06 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.52 (0.30), residues: 700 helix: -3.13 (0.97), residues: 26 sheet: -2.34 (0.34), residues: 217 loop : -2.38 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 149 HIS 0.004 0.001 HIS H 171 PHE 0.018 0.002 PHE A 515 TYR 0.008 0.001 TYR A 449 ARG 0.012 0.001 ARG H 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7596 (m) cc_final: 0.7297 (p) REVERT: H 43 LYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6517 (mmmm) REVERT: H 58 TYR cc_start: 0.8169 (m-80) cc_final: 0.7529 (m-80) REVERT: H 60 LEU cc_start: 0.7235 (tp) cc_final: 0.6895 (tp) REVERT: H 63 VAL cc_start: 0.7613 (t) cc_final: 0.7289 (p) REVERT: H 68 THR cc_start: 0.8090 (OUTLIER) cc_final: 0.7792 (m) REVERT: H 107 TYR cc_start: 0.7634 (OUTLIER) cc_final: 0.6645 (m-80) REVERT: H 149 VAL cc_start: 0.6910 (t) cc_final: 0.6689 (m) REVERT: A 347 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6054 (m-80) REVERT: A 355 ARG cc_start: 0.7875 (mmm160) cc_final: 0.7553 (mmm160) REVERT: A 356 LYS cc_start: 0.8258 (tmtp) cc_final: 0.7835 (tmtp) REVERT: A 382 VAL cc_start: 0.8578 (t) cc_final: 0.8156 (p) REVERT: A 386 LYS cc_start: 0.7696 (mttp) cc_final: 0.7344 (mttp) REVERT: A 398 ASP cc_start: 0.7656 (m-30) cc_final: 0.7266 (m-30) REVERT: A 428 ASP cc_start: 0.6958 (t0) cc_final: 0.6693 (t0) REVERT: A 439 ASN cc_start: 0.7783 (t0) cc_final: 0.7562 (t0) REVERT: A 440 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7588 (mmmt) REVERT: A 466 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7562 (tpp80) REVERT: A 471 GLU cc_start: 0.7332 (pp20) cc_final: 0.7007 (pp20) REVERT: A 535 LYS cc_start: 0.7638 (mtpp) cc_final: 0.6985 (ttmm) REVERT: A 536 ASN cc_start: 0.8244 (m-40) cc_final: 0.7777 (m110) REVERT: A 553 THR cc_start: 0.8460 (t) cc_final: 0.8219 (p) REVERT: A 558 LYS cc_start: 0.8370 (mptm) cc_final: 0.7777 (mptm) REVERT: A 573 THR cc_start: 0.7657 (m) cc_final: 0.7306 (p) REVERT: A 583 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6645 (tt0) outliers start: 43 outliers final: 32 residues processed: 179 average time/residue: 0.1996 time to fit residues: 44.7204 Evaluate side-chains 185 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.0970 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 339 HIS A 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.173937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.150853 restraints weight = 9206.632| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.26 r_work: 0.3823 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.6269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5591 Z= 0.229 Angle : 0.736 11.100 7608 Z= 0.365 Chirality : 0.047 0.215 845 Planarity : 0.006 0.059 981 Dihedral : 8.178 59.551 806 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.57 % Favored : 90.14 % Rotamer: Outliers : 7.01 % Allowed : 29.36 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.53 (0.30), residues: 700 helix: -3.10 (0.98), residues: 26 sheet: -2.50 (0.33), residues: 232 loop : -2.27 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 112 HIS 0.003 0.001 HIS H 171 PHE 0.020 0.002 PHE A 565 TYR 0.009 0.001 TYR L 141 ARG 0.012 0.001 ARG H 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3268.73 seconds wall clock time: 56 minutes 51.54 seconds (3411.54 seconds total)