Starting phenix.real_space_refine on Sun Apr 27 10:45:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdr_37143/04_2025/8kdr_37143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdr_37143/04_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_37143/04_2025/8kdr_37143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdr_37143/04_2025/8kdr_37143.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdr_37143/04_2025/8kdr_37143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdr_37143/04_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-5669/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: 4.00, per 1000 atoms: 0.73 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: 1.35 Conformation dependent library (CDL) restraints added in 693.0 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: 0.72 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: 1.46 Time building geometry restraints manager: 1.59 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.990 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.500 ------------------------------------------------------------------------------- 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 5600 Z= 0.699 Angle : 1.489 11.501 7626 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 Details of bonding type rmsd hydrogen bonds : bond 0.28080 ( 84) hydrogen bonds : angle 12.90591 ( 210) SS BOND : bond 0.01104 ( 9) SS BOND : angle 1.56557 ( 18) covalent geometry : bond 0.00960 ( 5591) covalent geometry : angle 1.48838 ( 7608) *********************** 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 : 0.590 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: 0.2023 time to fit residues: 71.9740 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 : 0.585 ------------------------------------------------------------------------------- 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: 0.0770 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: 0.8980 chunk 62 optimal weight: 4.9990 overall best weight: 0.2412 ------------------------------------------------------------------------------- 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 339 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4351 r_free = 0.4351 target = 0.185945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.164981 restraints weight = 9394.339| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 2.89 r_work: 0.3988 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 5600 Z= 0.147 Angle : 0.739 8.246 7626 Z= 0.383 Chirality : 0.048 0.255 845 Planarity : 0.006 0.057 981 Dihedral : 14.565 88.060 942 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.43 % Favored : 87.14 % Rotamer: Outliers : 14.03 % Allowed : 19.41 % Favored : 66.56 % 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 (0.64), residues: 26 sheet: -3.17 (0.32), residues: 177 loop : -3.69 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 97 HIS 0.016 0.002 HIS L 190 PHE 0.023 0.002 PHE A 429 TYR 0.019 0.002 TYR L 141 ARG 0.008 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 84) hydrogen bonds : angle 7.73437 ( 210) SS BOND : bond 0.01075 ( 9) SS BOND : angle 2.05424 ( 18) covalent geometry : bond 0.00328 ( 5591) covalent geometry : angle 0.73274 ( 7608) *********************** 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 237 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 151 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 46 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8075 (mt) REVERT: L 63 SER cc_start: 0.7332 (OUTLIER) cc_final: 0.6990 (p) REVERT: L 85 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.7022 (p) REVERT: L 99 PHE cc_start: 0.8009 (m-80) cc_final: 0.7694 (m-80) REVERT: L 177 SER cc_start: 0.8141 (t) cc_final: 0.7912 (p) REVERT: L 191 LYS cc_start: 0.6566 (mtmm) cc_final: 0.6061 (mtmm) REVERT: H 43 LYS cc_start: 0.6601 (OUTLIER) cc_final: 0.6323 (mmmm) REVERT: H 54 SER cc_start: 0.7348 (OUTLIER) cc_final: 0.7138 (p) REVERT: H 59 TYR cc_start: 0.8117 (m-80) cc_final: 0.7801 (m-80) REVERT: H 68 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7700 (m) REVERT: H 83 ASN cc_start: 0.6994 (m-40) cc_final: 0.6698 (m-40) REVERT: H 107 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6624 (m-80) REVERT: A 336 CYS cc_start: 0.5594 (OUTLIER) cc_final: 0.5219 (m) REVERT: A 350 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7932 (t) REVERT: A 356 LYS cc_start: 0.8101 (tmtp) cc_final: 0.7788 (tmtp) REVERT: A 365 TYR cc_start: 0.7882 (m-80) cc_final: 0.7372 (m-80) REVERT: A 371 PHE cc_start: 0.6265 (t80) cc_final: 0.6033 (t80) REVERT: A 386 LYS cc_start: 0.7618 (mttp) cc_final: 0.7371 (mttp) REVERT: A 402 ILE cc_start: 0.7541 (OUTLIER) cc_final: 0.7328 (pt) REVERT: A 418 ILE cc_start: 0.8580 (mm) cc_final: 0.8363 (mm) REVERT: A 428 ASP cc_start: 0.6843 (t0) cc_final: 0.6581 (t0) REVERT: A 440 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7473 (mmmt) REVERT: A 442 ASP cc_start: 0.7508 (m-30) cc_final: 0.7125 (m-30) REVERT: A 461 LEU cc_start: 0.7917 (tp) cc_final: 0.7566 (mp) REVERT: A 511 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7945 (t) REVERT: A 515 PHE cc_start: 0.7062 (m-80) cc_final: 0.6543 (m-80) REVERT: A 528 LYS cc_start: 0.6678 (OUTLIER) cc_final: 0.6353 (mtmt) REVERT: A 576 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7867 (t) outliers start: 86 outliers final: 41 residues processed: 209 average time/residue: 0.2094 time to fit residues: 53.8344 Evaluate side-chains 193 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 138 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.0370 overall best weight: 0.6660 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.177764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154382 restraints weight = 9193.290| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 3.22 r_work: 0.3855 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5600 Z= 0.205 Angle : 0.772 8.057 7626 Z= 0.398 Chirality : 0.049 0.232 845 Planarity : 0.006 0.053 981 Dihedral : 10.880 59.729 848 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.00 % Favored : 86.57 % Rotamer: Outliers : 11.26 % Allowed : 23.98 % 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: -4.71 (0.27), residues: 700 helix: -3.99 (0.59), residues: 38 sheet: -3.01 (0.30), residues: 213 loop : -3.26 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 97 HIS 0.014 0.002 HIS L 190 PHE 0.016 0.002 PHE L 83 TYR 0.019 0.002 TYR L 141 ARG 0.006 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 84) hydrogen bonds : angle 7.02600 ( 210) SS BOND : bond 0.00806 ( 9) SS BOND : angle 1.66350 ( 18) covalent geometry : bond 0.00464 ( 5591) covalent geometry : angle 0.76909 ( 7608) *********************** 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 207 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 138 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 46 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8417 (tp) REVERT: L 63 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7331 (p) REVERT: L 85 THR cc_start: 0.7658 (m) cc_final: 0.7331 (t) REVERT: L 99 PHE cc_start: 0.8068 (m-80) cc_final: 0.7739 (m-80) REVERT: L 191 LYS cc_start: 0.6582 (mtmm) cc_final: 0.6056 (mtmm) REVERT: H 32 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6325 (m-10) REVERT: H 68 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7946 (m) REVERT: H 92 MET cc_start: 0.7936 (tpp) cc_final: 0.7497 (tpp) REVERT: H 107 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: H 124 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7328 (mmmt) REVERT: H 173 PHE cc_start: 0.7242 (m-80) cc_final: 0.6983 (m-80) REVERT: A 353 TRP cc_start: 0.8194 (p-90) cc_final: 0.7750 (p-90) REVERT: A 355 ARG cc_start: 0.8071 (mmm160) cc_final: 0.7842 (mmm160) REVERT: A 356 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7741 (tmtp) REVERT: A 365 TYR cc_start: 0.8057 (m-80) cc_final: 0.7734 (m-80) REVERT: A 386 LYS cc_start: 0.7894 (mttp) cc_final: 0.7487 (mttp) REVERT: A 418 ILE cc_start: 0.8601 (mm) cc_final: 0.8392 (mm) REVERT: A 428 ASP cc_start: 0.7062 (t0) cc_final: 0.6750 (t0) REVERT: A 439 ASN cc_start: 0.8000 (t0) cc_final: 0.7629 (t0) REVERT: A 440 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7560 (mmmt) REVERT: A 455 LEU cc_start: 0.7721 (mp) cc_final: 0.7488 (mp) REVERT: A 511 VAL cc_start: 0.8259 (OUTLIER) cc_final: 0.8053 (t) REVERT: A 515 PHE cc_start: 0.6989 (m-80) cc_final: 0.6645 (m-80) REVERT: A 535 LYS cc_start: 0.7676 (mtpp) cc_final: 0.7407 (mtmm) REVERT: A 557 LYS cc_start: 0.8465 (mttt) cc_final: 0.8249 (mttt) REVERT: A 558 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8117 (mptm) REVERT: A 560 LEU cc_start: 0.9034 (mt) cc_final: 0.8829 (mm) REVERT: A 576 VAL cc_start: 0.8027 (OUTLIER) cc_final: 0.7772 (t) outliers start: 69 outliers final: 46 residues processed: 183 average time/residue: 0.2162 time to fit residues: 48.5338 Evaluate side-chains 188 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 131 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 190 HIS 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 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 124 LYS 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 326 ILE Chi-restraints excluded: chain A residue 332 ILE 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 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 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 558 LYS 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: 30.0000 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 5 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 167 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.176018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152445 restraints weight = 9421.686| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 3.29 r_work: 0.3836 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5600 Z= 0.183 Angle : 0.743 8.643 7626 Z= 0.378 Chirality : 0.049 0.248 845 Planarity : 0.006 0.058 981 Dihedral : 9.907 59.342 827 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.14 % Favored : 87.43 % Rotamer: Outliers : 11.09 % Allowed : 23.98 % 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: -4.30 (0.29), residues: 700 helix: -2.65 (1.20), residues: 20 sheet: -2.92 (0.31), residues: 218 loop : -2.99 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 97 HIS 0.013 0.002 HIS L 190 PHE 0.019 0.002 PHE A 371 TYR 0.015 0.002 TYR A 449 ARG 0.013 0.001 ARG H 97 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 84) hydrogen bonds : angle 6.57603 ( 210) SS BOND : bond 0.00634 ( 9) SS BOND : angle 1.58526 ( 18) covalent geometry : bond 0.00421 ( 5591) covalent geometry : angle 0.73958 ( 7608) *********************** 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 205 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 137 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 21 ILE cc_start: 0.8402 (mt) cc_final: 0.8186 (mm) REVERT: L 28 THR cc_start: 0.8420 (t) cc_final: 0.8205 (p) REVERT: L 46 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8383 (tp) REVERT: L 63 SER cc_start: 0.7640 (OUTLIER) cc_final: 0.7251 (p) REVERT: L 85 THR cc_start: 0.7660 (OUTLIER) cc_final: 0.7391 (p) REVERT: L 155 LEU cc_start: 0.1115 (OUTLIER) cc_final: 0.0734 (mt) REVERT: L 177 SER cc_start: 0.8166 (t) cc_final: 0.7847 (p) REVERT: L 191 LYS cc_start: 0.6596 (mtmm) cc_final: 0.5874 (mtmm) REVERT: H 43 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6509 (mmmm) REVERT: H 68 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7998 (m) REVERT: H 92 MET cc_start: 0.8038 (tpp) cc_final: 0.7617 (tpp) REVERT: H 107 TYR cc_start: 0.7681 (OUTLIER) cc_final: 0.6544 (m-80) REVERT: H 111 VAL cc_start: 0.8487 (t) cc_final: 0.8242 (m) REVERT: H 173 PHE cc_start: 0.7267 (m-80) cc_final: 0.6985 (m-80) REVERT: A 336 CYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5559 (m) REVERT: A 349 SER cc_start: 0.8577 (t) cc_final: 0.8348 (t) REVERT: A 353 TRP cc_start: 0.8326 (p-90) cc_final: 0.7970 (p-90) REVERT: A 356 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7777 (tmtp) REVERT: A 365 TYR cc_start: 0.8130 (m-80) cc_final: 0.7905 (m-80) REVERT: A 386 LYS cc_start: 0.7907 (mttp) cc_final: 0.7579 (mttp) REVERT: A 428 ASP cc_start: 0.6994 (t0) cc_final: 0.6687 (t0) REVERT: A 433 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8171 (p) REVERT: A 440 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7577 (mmmt) REVERT: A 455 LEU cc_start: 0.7549 (mp) cc_final: 0.7344 (mp) REVERT: A 515 PHE cc_start: 0.7081 (m-80) cc_final: 0.6815 (m-80) REVERT: A 535 LYS cc_start: 0.7655 (mtpp) cc_final: 0.6924 (mtpp) REVERT: A 536 ASN cc_start: 0.8167 (m-40) cc_final: 0.7837 (m110) REVERT: A 558 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8029 (mptm) outliers start: 68 outliers final: 40 residues processed: 180 average time/residue: 0.1990 time to fit residues: 44.7029 Evaluate side-chains 188 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 136 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 48 ILE 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 155 LEU 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 176 VAL 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 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 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 489 TYR Chi-restraints excluded: chain A residue 492 LEU 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 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS 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 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 23 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.174770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.151277 restraints weight = 9174.562| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.24 r_work: 0.3825 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5600 Z= 0.177 Angle : 0.730 9.022 7626 Z= 0.370 Chirality : 0.048 0.248 845 Planarity : 0.005 0.054 981 Dihedral : 9.303 57.356 823 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.57 % Favored : 87.00 % Rotamer: Outliers : 10.11 % Allowed : 24.96 % 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: -4.11 (0.29), residues: 700 helix: -3.18 (0.97), residues: 26 sheet: -2.74 (0.31), residues: 222 loop : -2.82 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 97 HIS 0.005 0.002 HIS H 35 PHE 0.015 0.002 PHE A 371 TYR 0.016 0.002 TYR L 193 ARG 0.009 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 84) hydrogen bonds : angle 6.38996 ( 210) SS BOND : bond 0.00796 ( 9) SS BOND : angle 1.71242 ( 18) covalent geometry : bond 0.00410 ( 5591) covalent geometry : angle 0.72581 ( 7608) *********************** 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 203 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 141 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 79 GLN cc_start: 0.7749 (pm20) cc_final: 0.7262 (pm20) REVERT: L 82 ASP cc_start: 0.6851 (m-30) cc_final: 0.6323 (m-30) REVERT: L 85 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7421 (p) REVERT: L 155 LEU cc_start: 0.1013 (OUTLIER) cc_final: 0.0707 (mt) REVERT: L 177 SER cc_start: 0.8207 (t) cc_final: 0.7868 (p) REVERT: H 13 GLN cc_start: 0.8850 (mt0) cc_final: 0.8633 (mt0) REVERT: H 43 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6402 (mmmm) REVERT: H 48 VAL cc_start: 0.4271 (OUTLIER) cc_final: 0.3016 (t) REVERT: H 107 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.6523 (m-80) REVERT: H 171 HIS cc_start: 0.6759 (m-70) cc_final: 0.6496 (m-70) REVERT: A 353 TRP cc_start: 0.8421 (p-90) cc_final: 0.8132 (p-90) REVERT: A 355 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7790 (mmm160) REVERT: A 356 LYS cc_start: 0.8202 (tmtp) cc_final: 0.7795 (tmtp) REVERT: A 364 ASP cc_start: 0.7516 (t0) cc_final: 0.7093 (t0) REVERT: A 386 LYS cc_start: 0.7893 (mttp) cc_final: 0.7546 (mttp) REVERT: A 428 ASP cc_start: 0.6971 (t0) cc_final: 0.6662 (t0) REVERT: A 440 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7545 (mmmt) REVERT: A 535 LYS cc_start: 0.7695 (mtpp) cc_final: 0.7194 (mtmm) REVERT: A 536 ASN cc_start: 0.8182 (m-40) cc_final: 0.7852 (m110) REVERT: A 543 PHE cc_start: 0.7808 (m-80) cc_final: 0.7571 (m-80) REVERT: A 544 ASN cc_start: 0.7402 (OUTLIER) cc_final: 0.7082 (t160) REVERT: A 558 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.7920 (mptm) REVERT: A 576 VAL cc_start: 0.7942 (m) cc_final: 0.7697 (t) outliers start: 62 outliers final: 40 residues processed: 177 average time/residue: 0.2072 time to fit residues: 45.6333 Evaluate side-chains 185 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 70 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 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 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 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 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 414 GLN 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 544 ASN Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS 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: 3.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN A 321 GLN A 343 ASN A 563 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.174345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.150853 restraints weight = 9153.315| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 3.27 r_work: 0.3819 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5600 Z= 0.189 Angle : 0.735 9.016 7626 Z= 0.376 Chirality : 0.048 0.257 845 Planarity : 0.006 0.055 981 Dihedral : 8.916 57.485 814 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.57 % Favored : 88.00 % Rotamer: Outliers : 9.30 % Allowed : 25.29 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.29), residues: 700 helix: -2.43 (1.22), residues: 20 sheet: -2.65 (0.32), residues: 219 loop : -2.78 (0.27), residues: 461 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 0.019 0.002 PHE A 515 TYR 0.019 0.002 TYR A 453 ARG 0.009 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.03181 ( 84) hydrogen bonds : angle 6.27510 ( 210) SS BOND : bond 0.00817 ( 9) SS BOND : angle 1.74643 ( 18) covalent geometry : bond 0.00439 ( 5591) covalent geometry : angle 0.73060 ( 7608) *********************** 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 200 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 28 THR cc_start: 0.8496 (t) cc_final: 0.8272 (p) REVERT: L 70 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6824 (m-30) REVERT: L 79 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6786 (pm20) REVERT: L 82 ASP cc_start: 0.6914 (m-30) cc_final: 0.6287 (m-30) REVERT: L 85 THR cc_start: 0.7686 (OUTLIER) cc_final: 0.7431 (p) REVERT: L 107 ILE cc_start: 0.6070 (OUTLIER) cc_final: 0.5603 (mp) REVERT: L 155 LEU cc_start: 0.1040 (OUTLIER) cc_final: 0.0751 (mt) REVERT: L 177 SER cc_start: 0.8226 (t) cc_final: 0.7855 (p) REVERT: H 13 GLN cc_start: 0.8756 (mt0) cc_final: 0.8538 (mt0) REVERT: H 43 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6415 (mmmm) REVERT: H 48 VAL cc_start: 0.4369 (OUTLIER) cc_final: 0.3016 (t) REVERT: H 107 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6445 (m-80) REVERT: H 171 HIS cc_start: 0.6669 (m-70) cc_final: 0.6403 (m-70) REVERT: A 349 SER cc_start: 0.8585 (t) cc_final: 0.8371 (t) REVERT: A 356 LYS cc_start: 0.8190 (tmtp) cc_final: 0.7761 (tmtp) REVERT: A 386 LYS cc_start: 0.7932 (mttp) cc_final: 0.7562 (mttp) REVERT: A 428 ASP cc_start: 0.7080 (t0) cc_final: 0.6747 (t0) REVERT: A 440 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7540 (mmmt) REVERT: A 535 LYS cc_start: 0.7688 (mtpp) cc_final: 0.7467 (mtmm) REVERT: A 543 PHE cc_start: 0.7859 (m-80) cc_final: 0.7492 (m-80) REVERT: A 558 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7928 (mptm) REVERT: A 576 VAL cc_start: 0.7990 (m) cc_final: 0.7749 (t) outliers start: 57 outliers final: 41 residues processed: 177 average time/residue: 0.2122 time to fit residues: 46.8349 Evaluate side-chains 189 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 138 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 70 ASP Chi-restraints excluded: chain L residue 74 THR 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 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 48 VAL Chi-restraints excluded: chain H residue 56 ASP 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 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 414 GLN 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 558 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.173455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.150492 restraints weight = 9196.352| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 3.16 r_work: 0.3818 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 5600 Z= 0.194 Angle : 0.753 10.725 7626 Z= 0.383 Chirality : 0.049 0.267 845 Planarity : 0.006 0.053 981 Dihedral : 8.694 57.729 814 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.43 % Favored : 87.29 % Rotamer: Outliers : 9.79 % Allowed : 24.96 % Favored : 65.25 % 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 (1.24), residues: 20 sheet: -2.40 (0.33), residues: 211 loop : -2.77 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 112 HIS 0.005 0.001 HIS H 35 PHE 0.018 0.002 PHE L 83 TYR 0.016 0.002 TYR L 141 ARG 0.007 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 84) hydrogen bonds : angle 6.23311 ( 210) SS BOND : bond 0.00711 ( 9) SS BOND : angle 1.80215 ( 18) covalent geometry : bond 0.00450 ( 5591) covalent geometry : angle 0.74893 ( 7608) *********************** 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 195 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 135 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 ASP cc_start: 0.6883 (m-30) cc_final: 0.6676 (m-30) REVERT: L 85 THR cc_start: 0.7701 (OUTLIER) cc_final: 0.7447 (p) REVERT: L 107 ILE cc_start: 0.5992 (OUTLIER) cc_final: 0.5774 (mp) REVERT: L 155 LEU cc_start: 0.0937 (OUTLIER) cc_final: 0.0683 (mt) REVERT: L 177 SER cc_start: 0.8280 (t) cc_final: 0.7906 (p) REVERT: H 13 GLN cc_start: 0.8701 (mt0) cc_final: 0.8462 (mt0) REVERT: H 43 LYS cc_start: 0.7033 (OUTLIER) cc_final: 0.6437 (mmmm) REVERT: H 56 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7049 (p0) REVERT: H 97 ARG cc_start: 0.8098 (ptt90) cc_final: 0.7609 (ppt170) REVERT: H 107 TYR cc_start: 0.7628 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: H 171 HIS cc_start: 0.6828 (m-70) cc_final: 0.6606 (m-70) REVERT: A 347 PHE cc_start: 0.7040 (OUTLIER) cc_final: 0.6354 (m-80) REVERT: A 349 SER cc_start: 0.8600 (t) cc_final: 0.8374 (t) REVERT: A 355 ARG cc_start: 0.8057 (mmm160) cc_final: 0.7736 (mmm160) REVERT: A 356 LYS cc_start: 0.8201 (tmtp) cc_final: 0.7785 (tmtp) REVERT: A 386 LYS cc_start: 0.7932 (mttp) cc_final: 0.7578 (mttp) REVERT: A 428 ASP cc_start: 0.7006 (t0) cc_final: 0.6704 (t0) REVERT: A 439 ASN cc_start: 0.7863 (t0) cc_final: 0.7615 (t0) REVERT: A 440 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7639 (mmmt) REVERT: A 449 TYR cc_start: 0.6527 (m-10) cc_final: 0.6318 (m-80) REVERT: A 535 LYS cc_start: 0.7685 (mtpp) cc_final: 0.7322 (ttmm) REVERT: A 543 PHE cc_start: 0.8110 (m-80) cc_final: 0.7733 (m-80) REVERT: A 558 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7922 (mptm) REVERT: A 576 VAL cc_start: 0.8043 (m) cc_final: 0.7812 (t) REVERT: A 583 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6491 (tt0) outliers start: 60 outliers final: 42 residues processed: 172 average time/residue: 0.2037 time to fit residues: 43.7210 Evaluate side-chains 184 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 132 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 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 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 48 VAL Chi-restraints excluded: chain H residue 56 ASP 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 110 ASP 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 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 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 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 558 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP 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: 0.9990 chunk 4 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 62 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.172726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.149670 restraints weight = 9255.889| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 3.17 r_work: 0.3820 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 5600 Z= 0.203 Angle : 0.749 10.142 7626 Z= 0.385 Chirality : 0.049 0.257 845 Planarity : 0.006 0.050 981 Dihedral : 8.555 56.830 812 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.43 % Favored : 87.29 % Rotamer: Outliers : 9.14 % Allowed : 25.61 % Favored : 65.25 % 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: -3.62 (0.30), residues: 700 helix: -2.41 (1.24), residues: 20 sheet: -2.21 (0.34), residues: 207 loop : -2.64 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 97 HIS 0.005 0.002 HIS H 35 PHE 0.017 0.002 PHE A 515 TYR 0.015 0.002 TYR L 141 ARG 0.006 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 84) hydrogen bonds : angle 6.31527 ( 210) SS BOND : bond 0.00678 ( 9) SS BOND : angle 1.73131 ( 18) covalent geometry : bond 0.00467 ( 5591) covalent geometry : angle 0.74470 ( 7608) *********************** 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 191 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 79 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: L 85 THR cc_start: 0.7683 (OUTLIER) cc_final: 0.7427 (p) REVERT: L 107 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5706 (mp) REVERT: L 155 LEU cc_start: 0.1015 (OUTLIER) cc_final: 0.0798 (mt) REVERT: L 177 SER cc_start: 0.8242 (t) cc_final: 0.7896 (p) REVERT: H 7 SER cc_start: 0.8276 (t) cc_final: 0.8060 (p) REVERT: H 43 LYS cc_start: 0.7047 (OUTLIER) cc_final: 0.6469 (mmmm) REVERT: H 56 ASP cc_start: 0.7614 (p0) cc_final: 0.7388 (p0) REVERT: H 107 TYR cc_start: 0.7667 (OUTLIER) cc_final: 0.6418 (m-80) REVERT: H 124 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7460 (mmmt) REVERT: A 347 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.6527 (m-80) REVERT: A 349 SER cc_start: 0.8572 (t) cc_final: 0.8341 (t) REVERT: A 355 ARG cc_start: 0.8123 (mmm160) cc_final: 0.7858 (mmm160) REVERT: A 356 LYS cc_start: 0.8228 (tmtp) cc_final: 0.7810 (tmtp) REVERT: A 382 VAL cc_start: 0.8646 (t) cc_final: 0.8228 (p) REVERT: A 386 LYS cc_start: 0.7969 (mttp) cc_final: 0.7603 (mttp) REVERT: A 428 ASP cc_start: 0.7010 (t0) cc_final: 0.6697 (t0) REVERT: A 439 ASN cc_start: 0.7871 (t0) cc_final: 0.7584 (t0) REVERT: A 440 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7648 (mmmt) REVERT: A 461 LEU cc_start: 0.7991 (tp) cc_final: 0.7780 (tp) REVERT: A 535 LYS cc_start: 0.7724 (mtpp) cc_final: 0.7409 (ttmm) REVERT: A 558 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7896 (mptm) REVERT: A 583 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6476 (tt0) outliers start: 56 outliers final: 41 residues processed: 170 average time/residue: 0.2144 time to fit residues: 45.1605 Evaluate side-chains 183 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 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 48 VAL 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 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 185 LEU 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 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 558 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP 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: 0.8980 chunk 21 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 12 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.173273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.150769 restraints weight = 9292.204| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 3.16 r_work: 0.3832 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 5600 Z= 0.192 Angle : 0.754 11.541 7626 Z= 0.385 Chirality : 0.049 0.263 845 Planarity : 0.006 0.054 981 Dihedral : 8.401 57.014 807 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.86 % Favored : 87.86 % Rotamer: Outliers : 8.65 % Allowed : 25.29 % Favored : 66.07 % 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: -3.55 (0.30), residues: 700 helix: -2.50 (1.19), residues: 20 sheet: -2.14 (0.35), residues: 207 loop : -2.60 (0.27), residues: 473 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 0.023 0.002 PHE A 456 TYR 0.015 0.002 TYR L 141 ARG 0.005 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.03217 ( 84) hydrogen bonds : angle 6.29091 ( 210) SS BOND : bond 0.00714 ( 9) SS BOND : angle 1.81417 ( 18) covalent geometry : bond 0.00446 ( 5591) covalent geometry : angle 0.74942 ( 7608) *********************** 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 192 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 139 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7686 (OUTLIER) cc_final: 0.7427 (p) REVERT: L 107 ILE cc_start: 0.5914 (OUTLIER) cc_final: 0.5674 (mp) REVERT: L 155 LEU cc_start: 0.0935 (OUTLIER) cc_final: 0.0724 (mt) REVERT: L 177 SER cc_start: 0.8255 (t) cc_final: 0.7904 (p) REVERT: H 13 GLN cc_start: 0.8694 (mt0) cc_final: 0.8472 (mt0) REVERT: H 43 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6507 (mmmm) REVERT: H 107 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: H 124 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7453 (mmmt) REVERT: H 149 VAL cc_start: 0.6875 (t) cc_final: 0.6623 (m) REVERT: A 347 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6496 (m-80) REVERT: A 349 SER cc_start: 0.8584 (t) cc_final: 0.8368 (t) REVERT: A 355 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7779 (mmm160) REVERT: A 356 LYS cc_start: 0.8241 (tmtp) cc_final: 0.7840 (tmtp) REVERT: A 382 VAL cc_start: 0.8625 (t) cc_final: 0.8196 (p) REVERT: A 386 LYS cc_start: 0.7948 (mttp) cc_final: 0.7577 (mttp) REVERT: A 428 ASP cc_start: 0.7000 (t0) cc_final: 0.6690 (t0) REVERT: A 439 ASN cc_start: 0.7854 (t0) cc_final: 0.7561 (t0) REVERT: A 440 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7607 (mmmt) REVERT: A 461 LEU cc_start: 0.7976 (tp) cc_final: 0.7738 (tp) REVERT: A 466 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7605 (tpp80) REVERT: A 535 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7376 (ttmm) REVERT: A 558 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7923 (mptm) REVERT: A 583 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6425 (tt0) outliers start: 53 outliers final: 41 residues processed: 172 average time/residue: 0.2080 time to fit residues: 44.4432 Evaluate side-chains 185 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 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 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 48 VAL Chi-restraints excluded: chain H residue 53 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 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 124 LYS 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 347 PHE 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 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 558 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP 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: 0.5980 chunk 20 optimal weight: 0.4980 chunk 55 optimal weight: 0.1980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 67 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.173516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.150394 restraints weight = 9347.372| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 3.26 r_work: 0.3816 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.6074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5600 Z= 0.177 Angle : 0.743 10.951 7626 Z= 0.380 Chirality : 0.048 0.249 845 Planarity : 0.006 0.052 981 Dihedral : 8.093 57.538 803 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.86 % Favored : 87.86 % Rotamer: Outliers : 8.32 % Allowed : 26.43 % Favored : 65.25 % 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: -3.51 (0.30), residues: 700 helix: -2.48 (1.19), residues: 20 sheet: -2.11 (0.34), residues: 216 loop : -2.56 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 149 HIS 0.005 0.001 HIS H 35 PHE 0.020 0.002 PHE A 456 TYR 0.016 0.002 TYR A 453 ARG 0.007 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 84) hydrogen bonds : angle 6.06793 ( 210) SS BOND : bond 0.00699 ( 9) SS BOND : angle 1.71075 ( 18) covalent geometry : bond 0.00415 ( 5591) covalent geometry : angle 0.73949 ( 7608) ********************** 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 188 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 79 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.7359 (pm20) REVERT: L 85 THR cc_start: 0.7669 (OUTLIER) cc_final: 0.7370 (p) REVERT: L 107 ILE cc_start: 0.5892 (OUTLIER) cc_final: 0.5672 (mp) REVERT: L 155 LEU cc_start: 0.0902 (OUTLIER) cc_final: 0.0701 (mt) REVERT: L 177 SER cc_start: 0.8260 (t) cc_final: 0.7931 (p) REVERT: H 13 GLN cc_start: 0.8699 (mt0) cc_final: 0.8475 (mt0) REVERT: H 43 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6452 (mmmm) REVERT: H 63 VAL cc_start: 0.7665 (t) cc_final: 0.7370 (p) REVERT: H 107 TYR cc_start: 0.7648 (OUTLIER) cc_final: 0.6438 (m-80) REVERT: H 124 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7438 (mmmt) REVERT: H 149 VAL cc_start: 0.6877 (t) cc_final: 0.6633 (m) REVERT: A 347 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6403 (m-80) REVERT: A 349 SER cc_start: 0.8579 (t) cc_final: 0.8356 (t) REVERT: A 355 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7767 (mmm160) REVERT: A 356 LYS cc_start: 0.8240 (tmtp) cc_final: 0.7826 (tmtp) REVERT: A 382 VAL cc_start: 0.8667 (t) cc_final: 0.8249 (p) REVERT: A 386 LYS cc_start: 0.7917 (mttp) cc_final: 0.7537 (mttp) REVERT: A 428 ASP cc_start: 0.7019 (t0) cc_final: 0.6706 (t0) REVERT: A 439 ASN cc_start: 0.7854 (t0) cc_final: 0.7577 (t0) REVERT: A 440 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7615 (mmmt) REVERT: A 461 LEU cc_start: 0.8028 (tp) cc_final: 0.7772 (tp) REVERT: A 466 ARG cc_start: 0.8013 (tpp80) cc_final: 0.7693 (tpp80) REVERT: A 472 ILE cc_start: 0.6987 (OUTLIER) cc_final: 0.6386 (tt) REVERT: A 535 LYS cc_start: 0.7727 (mtpp) cc_final: 0.7368 (ttmm) REVERT: A 543 PHE cc_start: 0.8194 (m-80) cc_final: 0.7755 (m-80) REVERT: A 558 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7913 (mptm) REVERT: A 583 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6465 (tt0) outliers start: 51 outliers final: 36 residues processed: 169 average time/residue: 0.2004 time to fit residues: 42.2456 Evaluate side-chains 185 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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 85 THR Chi-restraints excluded: chain L residue 107 ILE 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 53 THR 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 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 124 LYS 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 347 PHE 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 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 472 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 558 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP 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: 2.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.0470 chunk 24 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 38 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.173649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.150500 restraints weight = 9325.602| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 3.25 r_work: 0.3835 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.299 5600 Z= 0.378 Angle : 1.169 65.888 7626 Z= 0.674 Chirality : 0.047 0.237 845 Planarity : 0.011 0.278 981 Dihedral : 8.041 57.545 801 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.86 % Favored : 87.86 % Rotamer: Outliers : 7.99 % Allowed : 26.92 % Favored : 65.09 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.30), residues: 700 helix: -2.49 (1.19), residues: 20 sheet: -2.11 (0.34), residues: 216 loop : -2.56 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP L 97 HIS 0.005 0.001 HIS H 35 PHE 0.018 0.002 PHE A 515 TYR 0.014 0.002 TYR L 141 ARG 0.013 0.001 ARG A 457 Details of bonding type rmsd hydrogen bonds : bond 0.03077 ( 84) hydrogen bonds : angle 6.06645 ( 210) SS BOND : bond 0.00687 ( 9) SS BOND : angle 1.66247 ( 18) covalent geometry : bond 0.00807 ( 5591) covalent geometry : angle 1.16712 ( 7608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3126.44 seconds wall clock time: 54 minutes 33.68 seconds (3273.68 seconds total)