Starting phenix.real_space_refine on Fri Aug 22 15:55:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdr_37143/08_2025/8kdr_37143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdr_37143/08_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_37143/08_2025/8kdr_37143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdr_37143/08_2025/8kdr_37143.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdr_37143/08_2025/8kdr_37143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdr_37143/08_2025/8kdr_37143.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.36, per 1000 atoms: 0.25 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: 0.48 Conformation dependent library (CDL) restraints added in 148.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.19 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: 0.61 Time building geometry restraints manager: 0.61 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.680 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 10.670 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.000 ARG A 355 TYR 0.027 0.002 TYR H 152 PHE 0.035 0.003 PHE A 541 TRP 0.019 0.002 TRP A 353 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00960 ( 5591) covalent geometry : angle 1.48838 ( 7608) SS BOND : bond 0.01104 ( 9) SS BOND : angle 1.56557 ( 18) hydrogen bonds : bond 0.28080 ( 84) hydrogen bonds : angle 12.90591 ( 210) *********************** 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 : 0.183 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: 0.0868 time to fit residues: 31.1849 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 : 0.207 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 81 GLN H 207 HIS A 409 GLN A 414 GLN A 487 ASN A 544 ASN A 556 ASN A 563 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.183055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.162107 restraints weight = 9475.832| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 2.92 r_work: 0.3940 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.3125 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= 0.174 Angle : 0.770 8.489 7626 Z= 0.401 Chirality : 0.048 0.271 845 Planarity : 0.006 0.059 981 Dihedral : 14.762 84.564 942 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.86 % Favored : 86.71 % Rotamer: Outliers : 14.36 % Allowed : 20.39 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.06 (0.26), residues: 700 helix: -3.99 (0.66), residues: 26 sheet: -3.12 (0.32), residues: 182 loop : -3.69 (0.24), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 19 TYR 0.024 0.002 TYR L 141 PHE 0.024 0.002 PHE A 375 TRP 0.016 0.002 TRP L 97 HIS 0.016 0.003 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 5591) covalent geometry : angle 0.76427 ( 7608) SS BOND : bond 0.00674 ( 9) SS BOND : angle 2.07341 ( 18) hydrogen bonds : bond 0.03849 ( 84) hydrogen bonds : angle 7.76314 ( 210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 150 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 36 TYR cc_start: 0.8265 (m-80) cc_final: 0.7552 (m-80) REVERT: L 46 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8042 (mt) REVERT: L 63 SER cc_start: 0.7477 (OUTLIER) cc_final: 0.7140 (p) REVERT: L 85 THR cc_start: 0.7488 (OUTLIER) cc_final: 0.7203 (p) REVERT: L 99 PHE cc_start: 0.7992 (m-80) cc_final: 0.7711 (m-80) REVERT: L 177 SER cc_start: 0.8125 (t) cc_final: 0.7884 (p) REVERT: L 191 LYS cc_start: 0.6603 (mtmm) cc_final: 0.6103 (mtmm) REVERT: H 43 LYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6369 (mmmm) REVERT: H 68 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7821 (m) REVERT: H 107 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.7025 (m-80) REVERT: H 109 MET cc_start: 0.7729 (OUTLIER) cc_final: 0.7520 (mtt) REVERT: H 173 PHE cc_start: 0.7161 (m-80) cc_final: 0.6929 (m-80) REVERT: A 336 CYS cc_start: 0.5848 (OUTLIER) cc_final: 0.5341 (m) REVERT: A 350 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7980 (t) REVERT: A 356 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7841 (tmtp) REVERT: A 365 TYR cc_start: 0.7932 (m-80) cc_final: 0.7458 (m-80) REVERT: A 371 PHE cc_start: 0.6389 (t80) cc_final: 0.6146 (t80) REVERT: A 374 PHE cc_start: 0.7081 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: A 418 ILE cc_start: 0.8581 (mm) cc_final: 0.8342 (mm) REVERT: A 428 ASP cc_start: 0.6933 (t0) cc_final: 0.6630 (t0) REVERT: A 440 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7539 (mmmt) REVERT: A 442 ASP cc_start: 0.7542 (m-30) cc_final: 0.7145 (m-30) REVERT: A 466 ARG cc_start: 0.7098 (tpp80) cc_final: 0.6577 (mmm-85) REVERT: A 511 VAL cc_start: 0.8218 (OUTLIER) cc_final: 0.7975 (t) REVERT: A 515 PHE cc_start: 0.7045 (m-80) cc_final: 0.6539 (m-80) REVERT: A 528 LYS cc_start: 0.6696 (OUTLIER) cc_final: 0.6466 (mtmt) REVERT: A 576 VAL cc_start: 0.8086 (OUTLIER) cc_final: 0.7860 (t) outliers start: 88 outliers final: 45 residues processed: 206 average time/residue: 0.0913 time to fit residues: 23.2242 Evaluate side-chains 189 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 129 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 166 GLU 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 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 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 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 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 374 PHE 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 8 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN L 125 GLN L 167 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.177063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153666 restraints weight = 9158.371| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.19 r_work: 0.3845 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 5600 Z= 0.209 Angle : 0.771 7.925 7626 Z= 0.398 Chirality : 0.049 0.238 845 Planarity : 0.006 0.057 981 Dihedral : 11.634 73.297 857 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.43 % Allowed : 14.00 % Favored : 85.57 % Rotamer: Outliers : 11.42 % Allowed : 23.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.72 (0.27), residues: 700 helix: -3.97 (0.61), residues: 38 sheet: -2.97 (0.30), residues: 211 loop : -3.31 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 19 TYR 0.018 0.002 TYR H 94 PHE 0.020 0.002 PHE A 375 TRP 0.014 0.002 TRP L 97 HIS 0.014 0.002 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 5591) covalent geometry : angle 0.76747 ( 7608) SS BOND : bond 0.00694 ( 9) SS BOND : angle 1.62799 ( 18) hydrogen bonds : bond 0.03577 ( 84) hydrogen bonds : angle 7.11662 ( 210) *********************** 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 208 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 138 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: L 46 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8413 (tp) REVERT: L 63 SER cc_start: 0.7803 (OUTLIER) cc_final: 0.7312 (p) REVERT: L 79 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7050 (pm20) REVERT: L 81 GLU cc_start: 0.5621 (mp0) cc_final: 0.5320 (mp0) REVERT: L 85 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7346 (t) REVERT: L 99 PHE cc_start: 0.8041 (m-80) cc_final: 0.7741 (m-80) REVERT: L 124 GLU cc_start: 0.7294 (pm20) cc_final: 0.6761 (pm20) REVERT: L 177 SER cc_start: 0.8149 (t) cc_final: 0.7834 (p) REVERT: L 191 LYS cc_start: 0.6586 (mtmm) cc_final: 0.5832 (mtmm) REVERT: H 43 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6550 (mmmm) REVERT: H 68 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7958 (m) REVERT: H 92 MET cc_start: 0.7995 (tpp) cc_final: 0.7563 (tpp) REVERT: H 107 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: H 173 PHE cc_start: 0.7260 (m-80) cc_final: 0.6987 (m-80) REVERT: A 336 CYS cc_start: 0.5773 (OUTLIER) cc_final: 0.5554 (m) REVERT: A 353 TRP cc_start: 0.8188 (p-90) cc_final: 0.7742 (p-90) REVERT: A 355 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7791 (mmm160) REVERT: A 356 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7842 (tmtp) REVERT: A 365 TYR cc_start: 0.8086 (m-80) cc_final: 0.7789 (m-80) REVERT: A 371 PHE cc_start: 0.6657 (t80) cc_final: 0.6365 (t80) REVERT: A 374 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: A 386 LYS cc_start: 0.7899 (mttp) cc_final: 0.7581 (mttp) REVERT: A 418 ILE cc_start: 0.8573 (mm) cc_final: 0.8366 (mm) REVERT: A 428 ASP cc_start: 0.7001 (t0) cc_final: 0.6683 (t0) REVERT: A 440 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7562 (mmmt) REVERT: A 455 LEU cc_start: 0.7750 (mp) cc_final: 0.7525 (mp) REVERT: A 511 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.8069 (t) REVERT: A 515 PHE cc_start: 0.6992 (m-80) cc_final: 0.6670 (m-80) REVERT: A 535 LYS cc_start: 0.7692 (mtpp) cc_final: 0.7325 (mtpp) REVERT: A 557 LYS cc_start: 0.8463 (mttt) cc_final: 0.8254 (mttt) REVERT: A 558 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8135 (mptm) REVERT: A 560 LEU cc_start: 0.9045 (mt) cc_final: 0.8840 (mm) outliers start: 70 outliers final: 45 residues processed: 186 average time/residue: 0.0889 time to fit residues: 20.5755 Evaluate side-chains 187 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 129 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 166 GLU 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 41 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 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 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 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 46 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 0.0000 chunk 36 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 207 HIS 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 = 0.176614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.153235 restraints weight = 9280.423| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.27 r_work: 0.3839 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5600 Z= 0.187 Angle : 0.750 8.840 7626 Z= 0.380 Chirality : 0.049 0.245 845 Planarity : 0.005 0.061 981 Dihedral : 10.888 72.601 840 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.29 % Favored : 87.29 % Rotamer: Outliers : 10.77 % Allowed : 24.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.46 (0.28), residues: 700 helix: -3.16 (0.94), residues: 26 sheet: -2.98 (0.31), residues: 218 loop : -3.09 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 19 TYR 0.015 0.002 TYR A 449 PHE 0.017 0.002 PHE A 375 TRP 0.013 0.002 TRP L 97 HIS 0.007 0.002 HIS L 190 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 5591) covalent geometry : angle 0.74754 ( 7608) SS BOND : bond 0.00626 ( 9) SS BOND : angle 1.54568 ( 18) hydrogen bonds : bond 0.03186 ( 84) hydrogen bonds : angle 6.73833 ( 210) *********************** 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 203 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 137 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: L 28 THR cc_start: 0.8439 (t) cc_final: 0.8223 (p) REVERT: L 46 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8472 (tp) REVERT: L 63 SER cc_start: 0.7678 (OUTLIER) cc_final: 0.7280 (p) REVERT: L 85 THR cc_start: 0.7712 (m) cc_final: 0.7393 (p) REVERT: L 155 LEU cc_start: 0.1080 (OUTLIER) cc_final: 0.0706 (mt) REVERT: H 32 TYR cc_start: 0.7198 (OUTLIER) cc_final: 0.6984 (m-10) REVERT: H 43 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6346 (mmmm) REVERT: H 48 VAL cc_start: 0.3860 (OUTLIER) cc_final: 0.2629 (t) REVERT: H 92 MET cc_start: 0.8058 (tpp) cc_final: 0.7625 (tpp) REVERT: H 107 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.6520 (m-80) REVERT: H 173 PHE cc_start: 0.7294 (m-80) cc_final: 0.7016 (m-80) REVERT: A 349 SER cc_start: 0.8632 (t) cc_final: 0.8368 (t) REVERT: A 353 TRP cc_start: 0.8307 (p-90) cc_final: 0.7938 (p-90) REVERT: A 356 LYS cc_start: 0.8237 (tmtp) cc_final: 0.7817 (tmtp) REVERT: A 365 TYR cc_start: 0.8105 (m-80) cc_final: 0.7873 (m-80) REVERT: A 374 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: A 386 LYS cc_start: 0.7927 (mttp) cc_final: 0.7572 (mttp) REVERT: A 428 ASP cc_start: 0.6959 (t0) cc_final: 0.6628 (t0) REVERT: A 440 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7594 (mmmt) REVERT: A 455 LEU cc_start: 0.7601 (mp) cc_final: 0.7391 (mp) REVERT: A 461 LEU cc_start: 0.8070 (tp) cc_final: 0.7861 (tp) REVERT: A 515 PHE cc_start: 0.7044 (m-80) cc_final: 0.6775 (m-80) REVERT: A 535 LYS cc_start: 0.7693 (mtpp) cc_final: 0.7336 (mtpp) REVERT: A 558 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8043 (mptm) REVERT: A 576 VAL cc_start: 0.8013 (m) cc_final: 0.7752 (t) outliers start: 66 outliers final: 40 residues processed: 177 average time/residue: 0.0910 time to fit residues: 20.0811 Evaluate side-chains 178 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 74 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 54 SER 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 374 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 207 HIS ** 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 = 0.4225 r_free = 0.4225 target = 0.175480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.152089 restraints weight = 9443.617| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 3.34 r_work: 0.3826 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 5600 Z= 0.173 Angle : 0.728 8.659 7626 Z= 0.369 Chirality : 0.047 0.251 845 Planarity : 0.006 0.055 981 Dihedral : 9.215 58.107 825 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.14 % Favored : 87.43 % Rotamer: Outliers : 10.77 % Allowed : 24.47 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.20 (0.29), residues: 700 helix: -2.58 (1.23), residues: 20 sheet: -2.81 (0.31), residues: 218 loop : -2.94 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 3 TYR 0.011 0.002 TYR L 141 PHE 0.016 0.002 PHE L 83 TRP 0.012 0.002 TRP L 97 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 5591) covalent geometry : angle 0.72392 ( 7608) SS BOND : bond 0.00725 ( 9) SS BOND : angle 1.66460 ( 18) hydrogen bonds : bond 0.03158 ( 84) hydrogen bonds : angle 6.44124 ( 210) *********************** 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 208 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 142 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 46 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8448 (tp) REVERT: L 85 THR cc_start: 0.7662 (m) cc_final: 0.7370 (p) REVERT: L 155 LEU cc_start: 0.1009 (OUTLIER) cc_final: 0.0693 (mt) REVERT: L 177 SER cc_start: 0.8179 (t) cc_final: 0.7839 (p) REVERT: H 13 GLN cc_start: 0.8856 (mt0) cc_final: 0.8653 (mt0) REVERT: H 43 LYS cc_start: 0.6933 (OUTLIER) cc_final: 0.6339 (mmmm) REVERT: H 48 VAL cc_start: 0.4203 (OUTLIER) cc_final: 0.2957 (t) REVERT: H 92 MET cc_start: 0.8010 (tpp) cc_final: 0.7614 (tpp) REVERT: H 107 TYR cc_start: 0.7830 (OUTLIER) cc_final: 0.6410 (m-80) REVERT: A 349 SER cc_start: 0.8569 (t) cc_final: 0.8332 (t) REVERT: A 353 TRP cc_start: 0.8387 (p-90) cc_final: 0.8079 (p-90) REVERT: A 355 ARG cc_start: 0.8032 (mmm160) cc_final: 0.7754 (mmm160) REVERT: A 364 ASP cc_start: 0.7505 (t0) cc_final: 0.7131 (t0) REVERT: A 374 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: A 386 LYS cc_start: 0.7915 (mttp) cc_final: 0.7512 (mttp) REVERT: A 428 ASP cc_start: 0.6982 (t0) cc_final: 0.6664 (t0) REVERT: A 440 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7570 (mmmt) REVERT: A 461 LEU cc_start: 0.8191 (tp) cc_final: 0.7927 (tp) REVERT: A 511 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.8041 (t) REVERT: A 535 LYS cc_start: 0.7648 (mtpp) cc_final: 0.7034 (ttmm) REVERT: A 536 ASN cc_start: 0.8186 (m-40) cc_final: 0.7746 (m110) REVERT: A 543 PHE cc_start: 0.7744 (m-80) cc_final: 0.7429 (m-80) REVERT: A 544 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6886 (t160) REVERT: A 556 ASN cc_start: 0.7772 (t0) cc_final: 0.7241 (t0) REVERT: A 558 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7898 (mptm) outliers start: 66 outliers final: 39 residues processed: 184 average time/residue: 0.0914 time to fit residues: 21.0965 Evaluate side-chains 187 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 138 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 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 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 374 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 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 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 9 optimal weight: 0.0970 chunk 53 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN A 343 ASN 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 = 0.175293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.152623 restraints weight = 9274.060| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 3.10 r_work: 0.3847 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5600 Z= 0.169 Angle : 0.721 9.547 7626 Z= 0.366 Chirality : 0.047 0.253 845 Planarity : 0.005 0.051 981 Dihedral : 8.856 58.198 819 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.29 % Favored : 89.29 % Rotamer: Outliers : 9.30 % Allowed : 26.43 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.11 (0.29), residues: 700 helix: -2.46 (1.21), residues: 20 sheet: -2.76 (0.31), residues: 230 loop : -2.85 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 3 TYR 0.022 0.002 TYR A 453 PHE 0.019 0.002 PHE A 515 TRP 0.011 0.002 TRP L 97 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 5591) covalent geometry : angle 0.71753 ( 7608) SS BOND : bond 0.00720 ( 9) SS BOND : angle 1.65249 ( 18) hydrogen bonds : bond 0.03086 ( 84) hydrogen bonds : angle 6.26351 ( 210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 136 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 28 THR cc_start: 0.8505 (t) cc_final: 0.8299 (p) REVERT: L 82 ASP cc_start: 0.6814 (m-30) cc_final: 0.6540 (m-30) REVERT: L 85 THR cc_start: 0.7676 (m) cc_final: 0.7400 (p) REVERT: L 155 LEU cc_start: 0.0977 (OUTLIER) cc_final: 0.0697 (mt) REVERT: L 177 SER cc_start: 0.8248 (t) cc_final: 0.7883 (p) REVERT: H 13 GLN cc_start: 0.8766 (mt0) cc_final: 0.8547 (mt0) REVERT: H 19 ARG cc_start: 0.8433 (mmm160) cc_final: 0.8031 (mtp180) REVERT: H 43 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6390 (mmmm) REVERT: H 48 VAL cc_start: 0.4272 (OUTLIER) cc_final: 0.2873 (t) REVERT: H 92 MET cc_start: 0.7899 (tpp) cc_final: 0.7484 (tpp) REVERT: H 171 HIS cc_start: 0.6616 (m-70) cc_final: 0.6393 (m-70) REVERT: A 349 SER cc_start: 0.8587 (t) cc_final: 0.8384 (t) REVERT: A 364 ASP cc_start: 0.7453 (t0) cc_final: 0.7181 (t0) REVERT: A 382 VAL cc_start: 0.8482 (t) cc_final: 0.8077 (p) REVERT: A 428 ASP cc_start: 0.6996 (t0) cc_final: 0.6681 (t0) REVERT: A 440 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7540 (mmmt) REVERT: A 472 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6093 (tt) REVERT: A 511 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.8029 (t) REVERT: A 535 LYS cc_start: 0.7641 (mtpp) cc_final: 0.7371 (ttmm) REVERT: A 543 PHE cc_start: 0.7835 (m-80) cc_final: 0.7496 (m-80) REVERT: A 544 ASN cc_start: 0.7134 (OUTLIER) cc_final: 0.6881 (t160) REVERT: A 556 ASN cc_start: 0.7665 (t0) cc_final: 0.7101 (t0) REVERT: A 558 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7886 (mptm) REVERT: A 583 GLU cc_start: 0.6694 (OUTLIER) cc_final: 0.6449 (tt0) outliers start: 57 outliers final: 39 residues processed: 172 average time/residue: 0.0846 time to fit residues: 18.2435 Evaluate side-chains 182 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 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 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 472 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 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 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 583 GLU 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 34 optimal weight: 0.0170 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 0.0570 chunk 44 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.176361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.153288 restraints weight = 9505.786| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.25 r_work: 0.3849 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5600 Z= 0.150 Angle : 0.708 10.093 7626 Z= 0.357 Chirality : 0.047 0.256 845 Planarity : 0.005 0.047 981 Dihedral : 8.608 58.098 817 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.29 % Favored : 88.43 % Rotamer: Outliers : 9.62 % Allowed : 25.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.92 (0.29), residues: 700 helix: -2.43 (1.22), residues: 20 sheet: -2.58 (0.32), residues: 227 loop : -2.75 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 3 TYR 0.013 0.001 TYR L 141 PHE 0.018 0.002 PHE A 374 TRP 0.007 0.001 TRP L 97 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 5591) covalent geometry : angle 0.70396 ( 7608) SS BOND : bond 0.00820 ( 9) SS BOND : angle 1.67521 ( 18) hydrogen bonds : bond 0.02902 ( 84) hydrogen bonds : angle 6.05869 ( 210) *********************** 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 205 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 146 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 28 THR cc_start: 0.8528 (t) cc_final: 0.8278 (p) REVERT: L 82 ASP cc_start: 0.6938 (m-30) cc_final: 0.6629 (m-30) REVERT: L 85 THR cc_start: 0.7598 (m) cc_final: 0.7333 (p) REVERT: L 155 LEU cc_start: 0.0989 (OUTLIER) cc_final: 0.0743 (mt) REVERT: L 177 SER cc_start: 0.8230 (t) cc_final: 0.7891 (p) REVERT: H 19 ARG cc_start: 0.8471 (mmm160) cc_final: 0.7989 (mtp180) REVERT: H 43 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6436 (mmmm) REVERT: H 48 VAL cc_start: 0.4178 (OUTLIER) cc_final: 0.2945 (t) REVERT: H 56 ASP cc_start: 0.7689 (OUTLIER) cc_final: 0.7089 (p0) REVERT: H 60 LEU cc_start: 0.7408 (tp) cc_final: 0.6996 (tp) REVERT: H 92 MET cc_start: 0.7808 (tpp) cc_final: 0.7363 (tpp) REVERT: H 94 TYR cc_start: 0.8375 (m-80) cc_final: 0.8174 (m-80) REVERT: H 107 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6375 (m-80) REVERT: H 149 VAL cc_start: 0.6793 (t) cc_final: 0.6551 (m) REVERT: H 171 HIS cc_start: 0.6642 (m-70) cc_final: 0.6415 (m-70) REVERT: A 347 PHE cc_start: 0.7088 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: A 355 ARG cc_start: 0.7941 (mmm160) cc_final: 0.7710 (mmm160) REVERT: A 382 VAL cc_start: 0.8458 (t) cc_final: 0.8047 (p) REVERT: A 386 LYS cc_start: 0.7835 (mttp) cc_final: 0.7442 (mttp) REVERT: A 428 ASP cc_start: 0.7015 (t0) cc_final: 0.6717 (t0) REVERT: A 440 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7563 (mmmt) REVERT: A 535 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7015 (ttmm) REVERT: A 536 ASN cc_start: 0.8193 (m-40) cc_final: 0.7745 (m110) REVERT: A 543 PHE cc_start: 0.7862 (m-80) cc_final: 0.7424 (m-80) REVERT: A 544 ASN cc_start: 0.7142 (OUTLIER) cc_final: 0.6880 (t160) REVERT: A 556 ASN cc_start: 0.7683 (t0) cc_final: 0.7094 (t0) REVERT: A 558 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7888 (mptm) REVERT: A 583 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6541 (tt0) outliers start: 59 outliers final: 40 residues processed: 182 average time/residue: 0.0861 time to fit residues: 19.7331 Evaluate side-chains 193 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 143 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 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 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 67 optimal weight: 0.0070 chunk 28 optimal weight: 0.1980 chunk 11 optimal weight: 0.4980 overall best weight: 0.3798 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.176179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.153193 restraints weight = 9400.898| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 3.28 r_work: 0.3841 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 5600 Z= 0.148 Angle : 0.711 10.301 7626 Z= 0.357 Chirality : 0.047 0.240 845 Planarity : 0.005 0.045 981 Dihedral : 8.386 58.083 816 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.00 % Favored : 88.71 % Rotamer: Outliers : 7.99 % Allowed : 28.22 % Favored : 63.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.88 (0.29), residues: 700 helix: -2.44 (1.21), residues: 20 sheet: -2.54 (0.32), residues: 216 loop : -2.73 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 3 TYR 0.009 0.001 TYR A 453 PHE 0.017 0.002 PHE A 515 TRP 0.010 0.002 TRP L 97 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5591) covalent geometry : angle 0.70849 ( 7608) SS BOND : bond 0.00614 ( 9) SS BOND : angle 1.51468 ( 18) hydrogen bonds : bond 0.02908 ( 84) hydrogen bonds : angle 5.88481 ( 210) *********************** 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 196 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 82 ASP cc_start: 0.6984 (m-30) cc_final: 0.6658 (m-30) REVERT: L 85 THR cc_start: 0.7618 (m) cc_final: 0.7317 (p) REVERT: L 155 LEU cc_start: 0.0950 (OUTLIER) cc_final: 0.0709 (mt) REVERT: L 177 SER cc_start: 0.8192 (t) cc_final: 0.7895 (p) REVERT: H 4 LEU cc_start: 0.8939 (mp) cc_final: 0.8738 (mt) REVERT: H 19 ARG cc_start: 0.8424 (mmm160) cc_final: 0.8054 (mtp180) REVERT: H 48 VAL cc_start: 0.4255 (OUTLIER) cc_final: 0.3005 (t) REVERT: H 56 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7373 (p0) REVERT: H 60 LEU cc_start: 0.7329 (tp) cc_final: 0.6904 (tp) REVERT: H 92 MET cc_start: 0.7809 (tpp) cc_final: 0.7492 (tpp) REVERT: H 107 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.6346 (m-80) REVERT: H 124 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7394 (mmmt) REVERT: H 149 VAL cc_start: 0.6813 (t) cc_final: 0.6585 (m) REVERT: H 171 HIS cc_start: 0.6772 (m-70) cc_final: 0.6564 (m-70) REVERT: A 353 TRP cc_start: 0.8283 (p-90) cc_final: 0.8070 (p-90) REVERT: A 355 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7665 (mmm160) REVERT: A 356 LYS cc_start: 0.8254 (tmtp) cc_final: 0.7801 (tmtp) REVERT: A 386 LYS cc_start: 0.7836 (mttp) cc_final: 0.7437 (mttp) REVERT: A 428 ASP cc_start: 0.6986 (t0) cc_final: 0.6712 (t0) REVERT: A 440 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7555 (mmmt) REVERT: A 472 ILE cc_start: 0.6748 (OUTLIER) cc_final: 0.6045 (tt) REVERT: A 535 LYS cc_start: 0.7655 (mtpp) cc_final: 0.7069 (ttmm) REVERT: A 536 ASN cc_start: 0.8214 (m-40) cc_final: 0.7766 (m110) REVERT: A 543 PHE cc_start: 0.7984 (m-80) cc_final: 0.7585 (m-80) REVERT: A 544 ASN cc_start: 0.7164 (OUTLIER) cc_final: 0.6859 (t0) REVERT: A 556 ASN cc_start: 0.7693 (t0) cc_final: 0.7109 (t0) REVERT: A 558 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7868 (mptm) REVERT: A 583 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6547 (tt0) outliers start: 49 outliers final: 37 residues processed: 177 average time/residue: 0.0918 time to fit residues: 20.3422 Evaluate side-chains 192 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 145 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 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 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 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 472 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 66 optimal weight: 0.0020 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 28 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 overall best weight: 0.3966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.176392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.153278 restraints weight = 9359.305| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 3.26 r_work: 0.3847 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5600 Z= 0.149 Angle : 0.707 10.727 7626 Z= 0.357 Chirality : 0.046 0.240 845 Planarity : 0.006 0.058 981 Dihedral : 8.157 58.312 811 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.00 % Favored : 88.71 % Rotamer: Outliers : 7.50 % Allowed : 28.22 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.63 (0.30), residues: 700 helix: -3.13 (0.97), residues: 26 sheet: -2.31 (0.33), residues: 210 loop : -2.54 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 3 TYR 0.009 0.001 TYR L 141 PHE 0.018 0.002 PHE A 515 TRP 0.010 0.002 TRP L 97 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5591) covalent geometry : angle 0.70331 ( 7608) SS BOND : bond 0.00712 ( 9) SS BOND : angle 1.58058 ( 18) hydrogen bonds : bond 0.02769 ( 84) hydrogen bonds : angle 5.95048 ( 210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 28 THR cc_start: 0.8566 (t) cc_final: 0.8358 (p) REVERT: L 85 THR cc_start: 0.7603 (m) cc_final: 0.7327 (p) REVERT: L 124 GLU cc_start: 0.7466 (pm20) cc_final: 0.6771 (pm20) REVERT: L 155 LEU cc_start: 0.0985 (OUTLIER) cc_final: 0.0770 (mt) REVERT: L 177 SER cc_start: 0.8221 (t) cc_final: 0.7871 (p) REVERT: H 4 LEU cc_start: 0.8843 (mp) cc_final: 0.8590 (mt) REVERT: H 13 GLN cc_start: 0.8702 (mt0) cc_final: 0.8468 (mt0) REVERT: H 19 ARG cc_start: 0.8443 (mmm160) cc_final: 0.8053 (mtp180) REVERT: H 48 VAL cc_start: 0.4259 (OUTLIER) cc_final: 0.2920 (t) REVERT: H 56 ASP cc_start: 0.7663 (p0) cc_final: 0.7431 (p0) REVERT: H 60 LEU cc_start: 0.7291 (tp) cc_final: 0.6872 (tp) REVERT: H 107 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: H 124 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7318 (mmmt) REVERT: H 149 VAL cc_start: 0.6809 (t) cc_final: 0.6579 (m) REVERT: A 355 ARG cc_start: 0.7930 (mmm160) cc_final: 0.7708 (mmm160) REVERT: A 356 LYS cc_start: 0.8280 (tmtp) cc_final: 0.7827 (tmtp) REVERT: A 386 LYS cc_start: 0.7852 (mttp) cc_final: 0.7443 (mttp) REVERT: A 428 ASP cc_start: 0.6977 (t0) cc_final: 0.6709 (t0) REVERT: A 440 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7546 (mmmt) REVERT: A 472 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6024 (tt) REVERT: A 513 LEU cc_start: 0.7958 (mt) cc_final: 0.7695 (mt) REVERT: A 535 LYS cc_start: 0.7670 (mtpp) cc_final: 0.7117 (ttmm) REVERT: A 536 ASN cc_start: 0.8162 (m-40) cc_final: 0.7730 (m110) REVERT: A 543 PHE cc_start: 0.8002 (m-80) cc_final: 0.7514 (m-80) REVERT: A 556 ASN cc_start: 0.7721 (t0) cc_final: 0.7125 (t0) REVERT: A 558 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7891 (mptm) REVERT: A 583 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6559 (tt0) outliers start: 46 outliers final: 35 residues processed: 177 average time/residue: 0.0828 time to fit residues: 18.5746 Evaluate side-chains 185 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 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 472 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 583 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 26 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 1 optimal weight: 0.0470 chunk 67 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.174693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.151818 restraints weight = 9232.954| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 3.24 r_work: 0.3825 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5600 Z= 0.159 Angle : 0.735 10.903 7626 Z= 0.367 Chirality : 0.047 0.233 845 Planarity : 0.006 0.057 981 Dihedral : 8.149 58.400 807 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.00 % Favored : 88.71 % Rotamer: Outliers : 7.18 % Allowed : 28.55 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.30), residues: 700 helix: -3.11 (0.97), residues: 26 sheet: -2.34 (0.33), residues: 224 loop : -2.48 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 3 TYR 0.020 0.002 TYR A 453 PHE 0.019 0.002 PHE A 515 TRP 0.009 0.002 TRP H 112 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 5591) covalent geometry : angle 0.73115 ( 7608) SS BOND : bond 0.00653 ( 9) SS BOND : angle 1.62607 ( 18) hydrogen bonds : bond 0.02918 ( 84) hydrogen bonds : angle 5.98144 ( 210) ********************** 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: 44 poor density : 139 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7596 (m) cc_final: 0.7354 (p) REVERT: L 124 GLU cc_start: 0.7492 (pm20) cc_final: 0.7078 (pm20) REVERT: L 155 LEU cc_start: 0.0974 (OUTLIER) cc_final: 0.0765 (mt) REVERT: L 177 SER cc_start: 0.8221 (t) cc_final: 0.7904 (p) REVERT: H 13 GLN cc_start: 0.8666 (mt0) cc_final: 0.8402 (mt0) REVERT: H 43 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6748 (mmmm) REVERT: H 48 VAL cc_start: 0.4145 (OUTLIER) cc_final: 0.2919 (t) REVERT: H 60 LEU cc_start: 0.7309 (tp) cc_final: 0.6941 (tp) REVERT: H 107 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.6249 (m-80) REVERT: H 124 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7315 (mmmt) REVERT: H 149 VAL cc_start: 0.6891 (t) cc_final: 0.6647 (m) REVERT: A 356 LYS cc_start: 0.8273 (tmtp) cc_final: 0.7847 (tmtp) REVERT: A 382 VAL cc_start: 0.8487 (t) cc_final: 0.8055 (p) REVERT: A 386 LYS cc_start: 0.7894 (mttp) cc_final: 0.7481 (mttp) REVERT: A 428 ASP cc_start: 0.6979 (t0) cc_final: 0.6697 (t0) REVERT: A 440 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7541 (mmmt) REVERT: A 454 ARG cc_start: 0.7270 (mmt90) cc_final: 0.7033 (mtt-85) REVERT: A 472 ILE cc_start: 0.6617 (OUTLIER) cc_final: 0.5975 (tt) REVERT: A 535 LYS cc_start: 0.7683 (mtpp) cc_final: 0.7127 (ttmm) REVERT: A 536 ASN cc_start: 0.8158 (m-40) cc_final: 0.7724 (m110) REVERT: A 543 PHE cc_start: 0.8052 (m-80) cc_final: 0.7609 (m-80) REVERT: A 556 ASN cc_start: 0.7719 (t0) cc_final: 0.7133 (t0) REVERT: A 558 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7910 (mptm) REVERT: A 583 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6528 (tt0) outliers start: 44 outliers final: 34 residues processed: 170 average time/residue: 0.0821 time to fit residues: 17.3925 Evaluate side-chains 180 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 137 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 124 LYS Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 385 THR 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 468 ILE Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 583 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 34 optimal weight: 0.0870 chunk 20 optimal weight: 0.0470 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.175908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152734 restraints weight = 9299.034| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 3.27 r_work: 0.3836 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.5983 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= 0.142 Angle : 0.727 11.147 7626 Z= 0.364 Chirality : 0.047 0.222 845 Planarity : 0.006 0.055 981 Dihedral : 8.069 58.515 807 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.86 % Favored : 88.86 % Rotamer: Outliers : 6.69 % Allowed : 28.55 % Favored : 64.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.30), residues: 700 helix: -3.12 (0.97), residues: 26 sheet: -2.31 (0.33), residues: 214 loop : -2.42 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 3 TYR 0.017 0.001 TYR A 453 PHE 0.020 0.002 PHE A 515 TRP 0.008 0.001 TRP L 97 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5591) covalent geometry : angle 0.72411 ( 7608) SS BOND : bond 0.00602 ( 9) SS BOND : angle 1.53017 ( 18) hydrogen bonds : bond 0.02914 ( 84) hydrogen bonds : angle 5.89218 ( 210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1501.08 seconds wall clock time: 26 minutes 27.29 seconds (1587.29 seconds total)