Starting phenix.real_space_refine on Sat May 10 06:50:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdr_37143/05_2025/8kdr_37143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdr_37143/05_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_37143/05_2025/8kdr_37143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdr_37143/05_2025/8kdr_37143.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdr_37143/05_2025/8kdr_37143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdr_37143/05_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-5687/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: 3.86, per 1000 atoms: 0.71 Number of scatterers: 5454 At special positions: 0 Unit cell: (101.15, 94.01, 108.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1053 8.00 N 925 7.00 C 3455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 699.1 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: 0.66 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: 1.52 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.620 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.700 ------------------------------------------------------------------------------- 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 : 0.527 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: 0.1934 time to fit residues: 68.7300 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 : 0.593 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.164979 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 : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 46 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8076 (mt) REVERT: L 63 SER cc_start: 0.7331 (OUTLIER) cc_final: 0.6989 (p) REVERT: L 85 THR cc_start: 0.7294 (OUTLIER) cc_final: 0.7021 (p) REVERT: L 99 PHE cc_start: 0.8010 (m-80) cc_final: 0.7695 (m-80) REVERT: L 177 SER cc_start: 0.8142 (t) cc_final: 0.7913 (p) REVERT: L 191 LYS cc_start: 0.6567 (mtmm) cc_final: 0.6062 (mtmm) REVERT: H 43 LYS cc_start: 0.6599 (OUTLIER) cc_final: 0.6321 (mmmm) REVERT: H 54 SER cc_start: 0.7349 (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: 0.7701 (m) REVERT: H 83 ASN cc_start: 0.6998 (m-40) cc_final: 0.6702 (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: 0.5221 (m) REVERT: A 350 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7932 (t) REVERT: A 356 LYS cc_start: 0.8103 (tmtp) cc_final: 0.7789 (tmtp) REVERT: A 365 TYR cc_start: 0.7883 (m-80) cc_final: 0.7374 (m-80) REVERT: A 371 PHE cc_start: 0.6264 (t80) cc_final: 0.6033 (t80) REVERT: A 386 LYS cc_start: 0.7619 (mttp) cc_final: 0.7373 (mttp) REVERT: A 402 ILE cc_start: 0.7542 (OUTLIER) cc_final: 0.7330 (pt) REVERT: A 418 ILE cc_start: 0.8581 (mm) cc_final: 0.8364 (mm) REVERT: A 428 ASP cc_start: 0.6843 (t0) cc_final: 0.6581 (t0) REVERT: A 440 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7470 (mmmt) REVERT: A 442 ASP cc_start: 0.7505 (m-30) cc_final: 0.7121 (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: 0.7060 (m-80) cc_final: 0.6542 (m-80) REVERT: A 528 LYS cc_start: 0.6676 (OUTLIER) cc_final: 0.6351 (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: 0.2064 time to fit residues: 53.0977 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 : 0.561 ------------------------------------------------------------------------------- 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: 1.9990 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.175387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.152015 restraints weight = 9177.318| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.22 r_work: 0.3827 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 5600 Z= 0.249 Angle : 0.822 8.279 7626 Z= 0.426 Chirality : 0.051 0.239 845 Planarity : 0.006 0.056 981 Dihedral : 11.112 59.800 848 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.57 % Allowed : 13.57 % Favored : 85.86 % Rotamer: Outliers : 11.58 % Allowed : 24.47 % Favored : 63.95 % 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: -4.74 (0.27), residues: 700 helix: -3.96 (0.61), residues: 38 sheet: -3.04 (0.30), residues: 210 loop : -3.29 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP H 47 HIS 0.013 0.003 HIS L 190 PHE 0.019 0.002 PHE L 83 TYR 0.022 0.003 TYR H 94 ARG 0.008 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 84) hydrogen bonds : angle 7.29535 ( 210) SS BOND : bond 0.00681 ( 9) SS BOND : angle 1.71508 ( 18) covalent geometry : bond 0.00565 ( 5591) covalent geometry : angle 0.81888 ( 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 211 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 140 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 63 SER cc_start: 0.7880 (OUTLIER) cc_final: 0.7386 (p) REVERT: L 85 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7412 (t) REVERT: L 99 PHE cc_start: 0.8070 (m-80) cc_final: 0.7795 (m-80) REVERT: L 107 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6227 (mp) REVERT: L 124 GLU cc_start: 0.7294 (pm20) cc_final: 0.6833 (pm20) REVERT: L 191 LYS cc_start: 0.6577 (mtmm) cc_final: 0.6050 (mtmm) REVERT: H 7 SER cc_start: 0.8561 (p) cc_final: 0.8341 (p) REVERT: H 43 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6488 (mmmm) REVERT: H 68 THR cc_start: 0.8281 (OUTLIER) cc_final: 0.8034 (m) REVERT: H 92 MET cc_start: 0.7974 (tpp) cc_final: 0.7524 (tpp) REVERT: H 107 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: A 353 TRP cc_start: 0.8266 (p-90) cc_final: 0.7881 (p-90) REVERT: A 355 ARG cc_start: 0.8077 (mmm160) cc_final: 0.7835 (mmm160) REVERT: A 356 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7733 (tmtp) REVERT: A 365 TYR cc_start: 0.8117 (m-80) cc_final: 0.7846 (m-80) REVERT: A 386 LYS cc_start: 0.7944 (mttp) cc_final: 0.7523 (mttp) REVERT: A 428 ASP cc_start: 0.7132 (t0) cc_final: 0.6772 (t0) REVERT: A 439 ASN cc_start: 0.8043 (t0) cc_final: 0.7695 (t0) REVERT: A 440 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7597 (mmmt) REVERT: A 455 LEU cc_start: 0.7790 (mp) cc_final: 0.7573 (mp) REVERT: A 471 GLU cc_start: 0.7121 (pp20) cc_final: 0.6903 (pp20) REVERT: A 515 PHE cc_start: 0.6979 (m-80) cc_final: 0.6690 (m-80) REVERT: A 535 LYS cc_start: 0.7735 (mtpp) cc_final: 0.7345 (mtpp) REVERT: A 557 LYS cc_start: 0.8480 (mttt) cc_final: 0.8262 (mttt) REVERT: A 558 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8129 (mptm) REVERT: A 560 LEU cc_start: 0.9055 (mt) cc_final: 0.8854 (mm) REVERT: A 573 THR cc_start: 0.7409 (m) cc_final: 0.7137 (p) REVERT: A 576 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7802 (t) outliers start: 71 outliers final: 46 residues processed: 185 average time/residue: 0.2422 time to fit residues: 54.6859 Evaluate side-chains 190 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 134 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 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 109 MET Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 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 414 GLN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 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: 0.0070 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 15 optimal weight: 0.0010 chunk 33 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 overall best weight: 0.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN L 167 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS A 360 ASN A 388 ASN A 437 ASN A 540 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.179006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.155586 restraints weight = 9446.561| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 3.29 r_work: 0.3866 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5600 Z= 0.137 Angle : 0.708 8.511 7626 Z= 0.358 Chirality : 0.048 0.242 845 Planarity : 0.005 0.062 981 Dihedral : 9.962 58.502 831 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.71 % Favored : 89.86 % Rotamer: Outliers : 10.28 % Allowed : 24.14 % Favored : 65.58 % 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: -4.33 (0.28), residues: 700 helix: -3.30 (0.95), residues: 26 sheet: -2.90 (0.31), residues: 219 loop : -2.97 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 97 HIS 0.013 0.002 HIS L 190 PHE 0.019 0.002 PHE A 371 TYR 0.014 0.001 TYR A 449 ARG 0.005 0.001 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.02936 ( 84) hydrogen bonds : angle 6.39425 ( 210) SS BOND : bond 0.00564 ( 9) SS BOND : angle 1.52006 ( 18) covalent geometry : bond 0.00318 ( 5591) covalent geometry : angle 0.70543 ( 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 202 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 139 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: L 21 ILE cc_start: 0.8322 (mt) cc_final: 0.8112 (mm) REVERT: L 28 THR cc_start: 0.8396 (t) cc_final: 0.8184 (p) REVERT: L 63 SER cc_start: 0.7676 (OUTLIER) cc_final: 0.7293 (p) REVERT: L 79 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6663 (pm20) REVERT: L 82 ASP cc_start: 0.6600 (m-30) cc_final: 0.6243 (m-30) REVERT: L 85 THR cc_start: 0.7604 (m) cc_final: 0.7302 (p) REVERT: L 99 PHE cc_start: 0.8013 (m-80) cc_final: 0.7728 (m-80) REVERT: L 124 GLU cc_start: 0.7309 (pm20) cc_final: 0.6897 (pm20) REVERT: L 177 SER cc_start: 0.8173 (t) cc_final: 0.7837 (p) REVERT: L 191 LYS cc_start: 0.6550 (mtmm) cc_final: 0.5813 (mtmm) REVERT: H 43 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6485 (mmmm) REVERT: H 54 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7669 (p) REVERT: H 63 VAL cc_start: 0.7598 (t) cc_final: 0.7256 (p) REVERT: H 68 THR cc_start: 0.8148 (OUTLIER) cc_final: 0.7929 (m) REVERT: H 92 MET cc_start: 0.7924 (tpp) cc_final: 0.7531 (tpp) REVERT: H 107 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.6641 (m-80) REVERT: A 349 SER cc_start: 0.8453 (t) cc_final: 0.8235 (t) REVERT: A 353 TRP cc_start: 0.8284 (p-90) cc_final: 0.7902 (p-90) REVERT: A 355 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7707 (mmm160) REVERT: A 356 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.7753 (tmtp) REVERT: A 365 TYR cc_start: 0.8066 (m-80) cc_final: 0.7821 (m-80) REVERT: A 386 LYS cc_start: 0.7784 (mttp) cc_final: 0.7466 (mttp) REVERT: A 398 ASP cc_start: 0.7817 (m-30) cc_final: 0.7248 (m-30) REVERT: A 428 ASP cc_start: 0.6976 (t0) cc_final: 0.6677 (t0) REVERT: A 440 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7545 (mmmt) REVERT: A 471 GLU cc_start: 0.7166 (pp20) cc_final: 0.6886 (pp20) REVERT: A 515 PHE cc_start: 0.7062 (m-80) cc_final: 0.6777 (m-80) REVERT: A 535 LYS cc_start: 0.7632 (mtpp) cc_final: 0.7200 (mtmm) REVERT: A 536 ASN cc_start: 0.8199 (m-40) cc_final: 0.7903 (m110) REVERT: A 558 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8000 (mptm) REVERT: A 576 VAL cc_start: 0.8014 (m) cc_final: 0.7747 (t) outliers start: 63 outliers final: 33 residues processed: 183 average time/residue: 0.2159 time to fit residues: 49.5234 Evaluate side-chains 183 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 79 GLN 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 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 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 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 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 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: 1.9990 chunk 63 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 57 optimal weight: 0.0770 chunk 3 optimal weight: 0.5980 chunk 1 optimal weight: 0.0370 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 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 = 0.4255 r_free = 0.4255 target = 0.177777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.154490 restraints weight = 9140.976| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.24 r_work: 0.3852 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5600 Z= 0.147 Angle : 0.698 9.482 7626 Z= 0.354 Chirality : 0.047 0.248 845 Planarity : 0.005 0.051 981 Dihedral : 9.029 58.200 821 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.29 % Favored : 88.29 % Rotamer: Outliers : 9.14 % Allowed : 25.94 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.29), residues: 700 helix: -1.32 (1.63), residues: 14 sheet: -2.75 (0.32), residues: 207 loop : -2.84 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 97 HIS 0.006 0.001 HIS L 190 PHE 0.021 0.002 PHE A 371 TYR 0.019 0.001 TYR A 453 ARG 0.010 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 84) hydrogen bonds : angle 6.18476 ( 210) SS BOND : bond 0.00347 ( 9) SS BOND : angle 1.54735 ( 18) covalent geometry : bond 0.00346 ( 5591) covalent geometry : angle 0.69472 ( 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 198 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 142 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 21 ILE cc_start: 0.8485 (mt) cc_final: 0.8261 (mm) REVERT: L 85 THR cc_start: 0.7599 (m) cc_final: 0.7317 (p) REVERT: L 155 LEU cc_start: 0.0984 (OUTLIER) cc_final: 0.0652 (mt) REVERT: H 43 LYS cc_start: 0.6877 (OUTLIER) cc_final: 0.6466 (mmmm) REVERT: H 48 VAL cc_start: 0.4082 (OUTLIER) cc_final: 0.2854 (t) REVERT: H 60 LEU cc_start: 0.7422 (tp) cc_final: 0.6881 (tp) REVERT: H 63 VAL cc_start: 0.7581 (t) cc_final: 0.7262 (p) REVERT: H 92 MET cc_start: 0.7916 (tpp) cc_final: 0.7507 (tpp) REVERT: H 107 TYR cc_start: 0.7641 (OUTLIER) cc_final: 0.6511 (m-80) REVERT: A 349 SER cc_start: 0.8454 (t) cc_final: 0.8247 (t) REVERT: A 353 TRP cc_start: 0.8401 (p-90) cc_final: 0.8016 (p-90) REVERT: A 356 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7844 (tmtp) REVERT: A 386 LYS cc_start: 0.7834 (mttp) cc_final: 0.7472 (mttp) REVERT: A 398 ASP cc_start: 0.7788 (m-30) cc_final: 0.7469 (m-30) REVERT: A 428 ASP cc_start: 0.6938 (t0) cc_final: 0.6631 (t0) REVERT: A 440 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7511 (mmmt) REVERT: A 471 GLU cc_start: 0.7119 (pp20) cc_final: 0.6845 (pp20) REVERT: A 535 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7174 (mtmm) REVERT: A 536 ASN cc_start: 0.8192 (m-40) cc_final: 0.7888 (m110) REVERT: A 544 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6944 (t160) REVERT: A 556 ASN cc_start: 0.7789 (t0) cc_final: 0.7236 (t0) REVERT: A 558 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8008 (mptm) REVERT: A 576 VAL cc_start: 0.7967 (m) cc_final: 0.7717 (t) outliers start: 56 outliers final: 39 residues processed: 174 average time/residue: 0.2570 time to fit residues: 55.8558 Evaluate side-chains 186 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR 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 93 SER 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 119 ILE Chi-restraints excluded: chain H residue 128 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 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 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 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: 0.0770 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4224 r_free = 0.4224 target = 0.174680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.151427 restraints weight = 9275.862| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 3.21 r_work: 0.3812 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5600 Z= 0.183 Angle : 0.723 9.076 7626 Z= 0.370 Chirality : 0.048 0.253 845 Planarity : 0.005 0.048 981 Dihedral : 8.763 57.027 816 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.29 % Favored : 89.29 % Rotamer: Outliers : 9.62 % Allowed : 26.26 % Favored : 64.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.29), residues: 700 helix: -2.40 (1.24), residues: 20 sheet: -2.65 (0.32), residues: 219 loop : -2.77 (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 0.018 0.002 PHE A 371 TYR 0.011 0.002 TYR A 421 ARG 0.009 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.03302 ( 84) hydrogen bonds : angle 6.20219 ( 210) SS BOND : bond 0.00791 ( 9) SS BOND : angle 1.66011 ( 18) covalent geometry : bond 0.00423 ( 5591) covalent geometry : angle 0.71983 ( 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 206 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 147 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 79 GLN cc_start: 0.7318 (pm20) cc_final: 0.6844 (pm20) REVERT: L 82 ASP cc_start: 0.6836 (m-30) cc_final: 0.6503 (m-30) REVERT: L 85 THR cc_start: 0.7653 (m) cc_final: 0.7368 (p) REVERT: L 155 LEU cc_start: 0.0981 (OUTLIER) cc_final: 0.0682 (mt) REVERT: H 11 LEU cc_start: 0.8285 (tp) cc_final: 0.8045 (tt) REVERT: H 32 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6841 (m-10) REVERT: H 48 VAL cc_start: 0.4432 (OUTLIER) cc_final: 0.3082 (t) REVERT: H 56 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7160 (p0) REVERT: H 60 LEU cc_start: 0.7534 (tp) cc_final: 0.7080 (tp) REVERT: H 107 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.6427 (m-80) REVERT: H 149 VAL cc_start: 0.6646 (t) cc_final: 0.6409 (p) REVERT: A 349 SER cc_start: 0.8603 (t) cc_final: 0.8318 (t) REVERT: A 355 ARG cc_start: 0.8001 (mmm160) cc_final: 0.7743 (mmm160) REVERT: A 356 LYS cc_start: 0.8269 (tmtp) cc_final: 0.7847 (tmtp) REVERT: A 386 LYS cc_start: 0.7878 (mttp) cc_final: 0.7529 (mttp) REVERT: A 428 ASP cc_start: 0.6968 (t0) cc_final: 0.6656 (t0) REVERT: A 440 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7626 (mmmt) REVERT: A 471 GLU cc_start: 0.7107 (pp20) cc_final: 0.6736 (pp20) REVERT: A 535 LYS cc_start: 0.7659 (mtpp) cc_final: 0.7148 (mtmm) REVERT: A 536 ASN cc_start: 0.8242 (m-40) cc_final: 0.7889 (m110) REVERT: A 543 PHE cc_start: 0.7984 (m-80) cc_final: 0.7545 (m-80) REVERT: A 544 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.7039 (t160) REVERT: A 558 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7876 (mptm) REVERT: A 576 VAL cc_start: 0.7987 (m) cc_final: 0.7752 (t) outliers start: 59 outliers final: 38 residues processed: 184 average time/residue: 0.1889 time to fit residues: 43.5246 Evaluate side-chains 182 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 136 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 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 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER 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 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 560 LEU Chi-restraints excluded: chain A residue 565 PHE 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: 0.4980 chunk 42 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.175902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.152727 restraints weight = 9297.189| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 3.25 r_work: 0.3844 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 5600 Z= 0.150 Angle : 0.707 10.037 7626 Z= 0.357 Chirality : 0.047 0.254 845 Planarity : 0.005 0.059 981 Dihedral : 8.349 56.749 810 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.29 % Favored : 89.43 % Rotamer: Outliers : 8.97 % Allowed : 26.59 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.80 (0.29), residues: 700 helix: -2.43 (1.22), residues: 20 sheet: -2.43 (0.33), residues: 213 loop : -2.72 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 112 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.002 PHE A 515 TYR 0.010 0.001 TYR A 421 ARG 0.011 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 84) hydrogen bonds : angle 5.97010 ( 210) SS BOND : bond 0.00696 ( 9) SS BOND : angle 1.64220 ( 18) covalent geometry : bond 0.00357 ( 5591) covalent geometry : angle 0.70372 ( 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 194 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 139 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 ASP cc_start: 0.6962 (m-30) cc_final: 0.6636 (m-30) REVERT: L 85 THR cc_start: 0.7623 (m) cc_final: 0.7360 (p) REVERT: L 155 LEU cc_start: 0.0966 (OUTLIER) cc_final: 0.0715 (mt) REVERT: L 177 SER cc_start: 0.8238 (t) cc_final: 0.7866 (p) REVERT: H 43 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6411 (mmmm) REVERT: H 56 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7055 (p0) REVERT: H 60 LEU cc_start: 0.7388 (tp) cc_final: 0.6838 (tp) REVERT: H 63 VAL cc_start: 0.7606 (t) cc_final: 0.7278 (p) REVERT: H 107 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.6491 (m-80) REVERT: A 349 SER cc_start: 0.8552 (t) cc_final: 0.8261 (t) REVERT: A 355 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7688 (mmm160) REVERT: A 356 LYS cc_start: 0.8225 (tmtp) cc_final: 0.7796 (tmtp) REVERT: A 386 LYS cc_start: 0.7846 (mttp) cc_final: 0.7479 (mttp) REVERT: A 428 ASP cc_start: 0.6982 (t0) cc_final: 0.6681 (t0) REVERT: A 440 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7582 (mmmt) REVERT: A 471 GLU cc_start: 0.7151 (pp20) cc_final: 0.6755 (pp20) REVERT: A 535 LYS cc_start: 0.7637 (mtpp) cc_final: 0.7142 (mtmm) REVERT: A 536 ASN cc_start: 0.8239 (m-40) cc_final: 0.7893 (m110) REVERT: A 543 PHE cc_start: 0.7821 (m-80) cc_final: 0.7485 (m-80) REVERT: A 544 ASN cc_start: 0.7146 (OUTLIER) cc_final: 0.6929 (t160) REVERT: A 556 ASN cc_start: 0.7755 (t0) cc_final: 0.7121 (t0) REVERT: A 558 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7861 (mptm) REVERT: A 576 VAL cc_start: 0.7939 (m) cc_final: 0.7689 (t) outliers start: 55 outliers final: 43 residues processed: 173 average time/residue: 0.2032 time to fit residues: 43.8308 Evaluate side-chains 187 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR 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 101 GLN Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 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 350 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 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 544 ASN 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 569 ILE 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: 0.9980 chunk 4 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 42 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.174804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.151396 restraints weight = 9252.803| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 3.24 r_work: 0.3809 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.5622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5600 Z= 0.174 Angle : 0.722 9.827 7626 Z= 0.369 Chirality : 0.048 0.251 845 Planarity : 0.005 0.056 981 Dihedral : 8.267 56.622 810 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.86 % Favored : 88.86 % Rotamer: Outliers : 8.65 % Allowed : 26.75 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.30), residues: 700 helix: -3.11 (0.98), residues: 26 sheet: -2.33 (0.33), residues: 215 loop : -2.52 (0.28), residues: 459 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 0.019 0.002 PHE A 515 TYR 0.014 0.002 TYR A 453 ARG 0.008 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 84) hydrogen bonds : angle 5.97932 ( 210) SS BOND : bond 0.00639 ( 9) SS BOND : angle 1.62947 ( 18) covalent geometry : bond 0.00409 ( 5591) covalent geometry : angle 0.71889 ( 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: 53 poor density : 138 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7620 (m) cc_final: 0.7365 (p) REVERT: L 155 LEU cc_start: 0.0917 (OUTLIER) cc_final: 0.0688 (mt) REVERT: L 177 SER cc_start: 0.8199 (t) cc_final: 0.7877 (p) REVERT: H 43 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6342 (mmmm) REVERT: H 56 ASP cc_start: 0.7651 (p0) cc_final: 0.7426 (p0) REVERT: H 60 LEU cc_start: 0.7378 (tp) cc_final: 0.6837 (tp) REVERT: H 63 VAL cc_start: 0.7641 (t) cc_final: 0.7347 (p) REVERT: H 107 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6411 (m-80) REVERT: A 349 SER cc_start: 0.8518 (t) cc_final: 0.8210 (t) REVERT: A 356 LYS cc_start: 0.8300 (tmtp) cc_final: 0.7875 (tmtp) REVERT: A 386 LYS cc_start: 0.7855 (mttp) cc_final: 0.7470 (mttp) REVERT: A 428 ASP cc_start: 0.6957 (t0) cc_final: 0.6660 (t0) REVERT: A 440 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7581 (mmmt) REVERT: A 466 ARG cc_start: 0.7841 (tpp80) cc_final: 0.7506 (tpp80) REVERT: A 471 GLU cc_start: 0.7204 (pp20) cc_final: 0.6721 (pp20) REVERT: A 535 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7153 (mtmm) REVERT: A 536 ASN cc_start: 0.8277 (m-40) cc_final: 0.7920 (m110) REVERT: A 543 PHE cc_start: 0.8025 (m-80) cc_final: 0.7616 (m-80) REVERT: A 544 ASN cc_start: 0.7178 (OUTLIER) cc_final: 0.6908 (t160) REVERT: A 556 ASN cc_start: 0.7740 (t0) cc_final: 0.7118 (t0) REVERT: A 558 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7884 (mptm) REVERT: A 583 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6458 (tt0) outliers start: 53 outliers final: 40 residues processed: 172 average time/residue: 0.2068 time to fit residues: 44.0634 Evaluate side-chains 180 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 133 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR 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 101 GLN Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 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 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 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 544 ASN 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: 0.7980 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 59 optimal weight: 0.0270 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 422 ASN ** 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 = 0.4220 r_free = 0.4220 target = 0.174774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.151264 restraints weight = 9315.397| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.30 r_work: 0.3823 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.5801 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= 0.181 Angle : 0.735 11.349 7626 Z= 0.374 Chirality : 0.048 0.255 845 Planarity : 0.006 0.054 981 Dihedral : 8.210 57.207 806 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.00 % Favored : 88.71 % Rotamer: Outliers : 7.50 % Allowed : 27.08 % 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: -3.51 (0.30), residues: 700 helix: -2.39 (1.24), residues: 20 sheet: -2.25 (0.33), residues: 213 loop : -2.49 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 97 HIS 0.005 0.001 HIS H 35 PHE 0.021 0.002 PHE A 456 TYR 0.014 0.002 TYR A 453 ARG 0.008 0.001 ARG H 3 Details of bonding type rmsd hydrogen bonds : bond 0.03089 ( 84) hydrogen bonds : angle 6.12184 ( 210) SS BOND : bond 0.00723 ( 9) SS BOND : angle 1.74355 ( 18) covalent geometry : bond 0.00427 ( 5591) covalent geometry : angle 0.73074 ( 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 187 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7627 (m) cc_final: 0.7351 (p) REVERT: L 155 LEU cc_start: 0.0899 (OUTLIER) cc_final: 0.0678 (mt) REVERT: L 177 SER cc_start: 0.8236 (t) cc_final: 0.7871 (p) REVERT: H 43 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6365 (mmmm) REVERT: H 60 LEU cc_start: 0.7374 (tp) cc_final: 0.6812 (tp) REVERT: H 63 VAL cc_start: 0.7622 (t) cc_final: 0.7333 (p) REVERT: H 107 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6401 (m-80) REVERT: H 149 VAL cc_start: 0.6758 (t) cc_final: 0.6522 (m) REVERT: A 349 SER cc_start: 0.8507 (t) cc_final: 0.8277 (t) REVERT: A 355 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7678 (mmm160) REVERT: A 356 LYS cc_start: 0.8269 (tmtp) cc_final: 0.7832 (tmtp) REVERT: A 382 VAL cc_start: 0.8510 (t) cc_final: 0.8073 (p) REVERT: A 386 LYS cc_start: 0.7899 (mttp) cc_final: 0.7462 (mttp) REVERT: A 428 ASP cc_start: 0.7005 (t0) cc_final: 0.6699 (t0) REVERT: A 440 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7575 (mmmt) REVERT: A 466 ARG cc_start: 0.7888 (tpp80) cc_final: 0.7564 (tpp80) REVERT: A 471 GLU cc_start: 0.7208 (pp20) cc_final: 0.6810 (pp20) REVERT: A 513 LEU cc_start: 0.8051 (mt) cc_final: 0.7805 (mt) REVERT: A 535 LYS cc_start: 0.7690 (mtpp) cc_final: 0.7353 (ttmm) REVERT: A 543 PHE cc_start: 0.8060 (m-80) cc_final: 0.7600 (m-80) REVERT: A 544 ASN cc_start: 0.7229 (OUTLIER) cc_final: 0.6937 (t0) REVERT: A 556 ASN cc_start: 0.7745 (t0) cc_final: 0.7131 (t0) REVERT: A 558 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7898 (mptm) REVERT: A 583 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6394 (tt0) outliers start: 46 outliers final: 39 residues processed: 172 average time/residue: 0.2020 time to fit residues: 43.2706 Evaluate side-chains 187 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR 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 101 GLN Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 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 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 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 544 ASN 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: 0.6980 chunk 20 optimal weight: 0.0670 chunk 55 optimal weight: 0.0770 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 59 optimal weight: 0.0370 chunk 28 optimal weight: 1.9990 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** 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 = 0.4241 r_free = 0.4241 target = 0.176443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.152966 restraints weight = 9397.670| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 3.32 r_work: 0.3845 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5600 Z= 0.135 Angle : 0.698 10.179 7626 Z= 0.354 Chirality : 0.046 0.230 845 Planarity : 0.006 0.071 981 Dihedral : 7.935 57.918 804 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.00 % Favored : 90.71 % Rotamer: Outliers : 7.01 % Allowed : 27.90 % Favored : 65.09 % 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: -3.39 (0.30), residues: 700 helix: -2.43 (1.21), residues: 20 sheet: -2.18 (0.34), residues: 217 loop : -2.39 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 353 HIS 0.004 0.001 HIS H 171 PHE 0.019 0.002 PHE A 515 TYR 0.014 0.001 TYR A 453 ARG 0.010 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 84) hydrogen bonds : angle 5.87404 ( 210) SS BOND : bond 0.00641 ( 9) SS BOND : angle 1.52248 ( 18) covalent geometry : bond 0.00322 ( 5591) covalent geometry : angle 0.69450 ( 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 183 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 140 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7607 (m) cc_final: 0.7290 (p) REVERT: L 155 LEU cc_start: 0.0878 (OUTLIER) cc_final: 0.0667 (mt) REVERT: L 177 SER cc_start: 0.8239 (t) cc_final: 0.7882 (p) REVERT: H 43 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6666 (mmmm) REVERT: H 107 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6422 (m-80) REVERT: A 349 SER cc_start: 0.8467 (t) cc_final: 0.8259 (t) REVERT: A 353 TRP cc_start: 0.8177 (p-90) cc_final: 0.7843 (p-90) REVERT: A 355 ARG cc_start: 0.7830 (mmm160) cc_final: 0.7622 (mmm160) REVERT: A 356 LYS cc_start: 0.8260 (tmtp) cc_final: 0.7818 (tmtp) REVERT: A 382 VAL cc_start: 0.8519 (t) cc_final: 0.8095 (p) REVERT: A 386 LYS cc_start: 0.7837 (mttp) cc_final: 0.7399 (mttp) REVERT: A 428 ASP cc_start: 0.7001 (t0) cc_final: 0.6729 (t0) REVERT: A 440 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7531 (mmmt) REVERT: A 466 ARG cc_start: 0.7810 (tpp80) cc_final: 0.7573 (tpp80) REVERT: A 471 GLU cc_start: 0.7255 (pp20) cc_final: 0.6878 (pp20) REVERT: A 513 LEU cc_start: 0.7990 (mt) cc_final: 0.7747 (mt) REVERT: A 535 LYS cc_start: 0.7681 (mtpp) cc_final: 0.7000 (ttmm) REVERT: A 536 ASN cc_start: 0.8264 (m-40) cc_final: 0.7793 (m110) REVERT: A 543 PHE cc_start: 0.8002 (m-80) cc_final: 0.7565 (m-80) REVERT: A 544 ASN cc_start: 0.7155 (OUTLIER) cc_final: 0.6868 (t0) REVERT: A 558 LYS cc_start: 0.8425 (mptm) cc_final: 0.7886 (mptm) outliers start: 43 outliers final: 33 residues processed: 168 average time/residue: 0.2143 time to fit residues: 44.5064 Evaluate side-chains 176 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR 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 101 GLN Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 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 544 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 34 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.0980 chunk 24 optimal weight: 0.5980 chunk 42 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 38 optimal weight: 0.0370 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.2258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.176938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.153720 restraints weight = 9242.650| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 3.31 r_work: 0.3858 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 5600 Z= 0.125 Angle : 0.686 9.395 7626 Z= 0.347 Chirality : 0.046 0.214 845 Planarity : 0.006 0.069 981 Dihedral : 7.615 58.755 798 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.43 % Favored : 90.29 % Rotamer: Outliers : 6.20 % Allowed : 28.38 % 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: -3.29 (0.30), residues: 700 helix: -2.42 (1.21), residues: 20 sheet: -2.11 (0.34), residues: 217 loop : -2.31 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.005 0.001 HIS H 171 PHE 0.022 0.002 PHE A 456 TYR 0.014 0.001 TYR A 495 ARG 0.011 0.001 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 84) hydrogen bonds : angle 5.65196 ( 210) SS BOND : bond 0.00576 ( 9) SS BOND : angle 1.42610 ( 18) covalent geometry : bond 0.00299 ( 5591) covalent geometry : angle 0.68343 ( 7608) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.28 seconds wall clock time: 53 minutes 48.60 seconds (3228.60 seconds total)