Starting phenix.real_space_refine on Fri Dec 27 14:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdr_37143/12_2024/8kdr_37143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdr_37143/12_2024/8kdr_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_37143/12_2024/8kdr_37143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdr_37143/12_2024/8kdr_37143.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdr_37143/12_2024/8kdr_37143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdr_37143/12_2024/8kdr_37143.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 3455 2.51 5 N 925 2.21 5 O 1053 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5454 Number of models: 1 Model: "" Number of chains: 3 Chain: "L" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 13, 'TRANS': 198} Chain: "H" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1639 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "A" Number of atoms: 2184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2184 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 18, 'TRANS': 257} Time building chain proxies: 3.87, per 1000 atoms: 0.71 Number of scatterers: 5454 At special positions: 0 Unit cell: (101.15, 94.01, 108.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 21 16.00 O 1053 8.00 N 925 7.00 C 3455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 654.3 milliseconds 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 13 sheets defined 3.4% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.619A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 129 removed outlier: 3.894A pdb=" N LEU L 126 " --> pdb=" O SER L 122 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS L 127 " --> pdb=" O ASP L 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.911A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.741A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.748A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE L 21 " --> pdb=" O LEU L 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 11 removed outlier: 5.951A pdb=" N HIS L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU L 46 " --> pdb=" O HIS L 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.560A pdb=" N PHE L 117 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU L 136 " --> pdb=" O PHE L 117 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER L 178 " --> pdb=" O CYS L 135 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 146 through 151 removed outlier: 3.724A pdb=" N LYS L 146 " --> pdb=" O THR L 198 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR L 198 " --> pdb=" O LYS L 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN L 148 " --> pdb=" O GLU L 196 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 150 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA L 194 " --> pdb=" O LYS L 150 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LYS L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.590A pdb=" N ARG H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AA7, first strand: chain 'H' and resid 127 through 131 removed outlier: 3.943A pdb=" N GLY H 146 " --> pdb=" O LEU H 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 171 through 173 removed outlier: 4.008A pdb=" N VAL H 188 " --> pdb=" O HIS H 171 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER H 186 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.843A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.843A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.800A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.583A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 539 through 541 88 hydrogen bonds defined for protein. 210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.49 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 985 1.32 - 1.45: 1492 1.45 - 1.57: 3090 1.57 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 5591 Sorted by residual: bond pdb=" CA SER H 184 " pdb=" CB SER H 184 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.35e-02 5.49e+03 2.07e+01 bond pdb=" N PHE A 329 " pdb=" CA PHE A 329 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.78e+01 bond pdb=" N ILE H 119 " pdb=" CA ILE H 119 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.23e+01 bond pdb=" CA SER L 14 " pdb=" CB SER L 14 " ideal model delta sigma weight residual 1.535 1.468 0.067 1.93e-02 2.68e+03 1.20e+01 bond pdb=" CA SER L 7 " pdb=" CB SER L 7 " ideal model delta sigma weight residual 1.528 1.474 0.054 1.62e-02 3.81e+03 1.10e+01 ... (remaining 5586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 6674 2.30 - 4.60: 831 4.60 - 6.90: 85 6.90 - 9.20: 14 9.20 - 11.50: 4 Bond angle restraints: 7608 Sorted by residual: angle pdb=" N LEU H 166 " pdb=" CA LEU H 166 " pdb=" C LEU H 166 " ideal model delta sigma weight residual 111.82 103.35 8.47 1.16e+00 7.43e-01 5.33e+01 angle pdb=" CA PHE A 541 " pdb=" CB PHE A 541 " pdb=" CG PHE A 541 " ideal model delta sigma weight residual 113.80 120.37 -6.57 1.00e+00 1.00e+00 4.32e+01 angle pdb=" C THR L 53 " pdb=" CA THR L 53 " pdb=" CB THR L 53 " ideal model delta sigma weight residual 111.41 101.68 9.73 1.65e+00 3.67e-01 3.48e+01 angle pdb=" CA PHE A 565 " pdb=" CB PHE A 565 " pdb=" CG PHE A 565 " ideal model delta sigma weight residual 113.80 119.58 -5.78 1.00e+00 1.00e+00 3.34e+01 angle pdb=" CA PHE A 374 " pdb=" CB PHE A 374 " pdb=" CG PHE A 374 " ideal model delta sigma weight residual 113.80 119.51 -5.71 1.00e+00 1.00e+00 3.26e+01 ... (remaining 7603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 2855 16.61 - 33.23: 246 33.23 - 49.84: 157 49.84 - 66.45: 74 66.45 - 83.06: 6 Dihedral angle restraints: 3338 sinusoidal: 1293 harmonic: 2045 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -155.84 69.84 1 1.00e+01 1.00e-02 6.29e+01 dihedral pdb=" C SER L 94 " pdb=" N SER L 94 " pdb=" CA SER L 94 " pdb=" CB SER L 94 " ideal model delta harmonic sigma weight residual -122.60 -139.88 17.28 0 2.50e+00 1.60e-01 4.78e+01 dihedral pdb=" N SER L 94 " pdb=" C SER L 94 " pdb=" CA SER L 94 " pdb=" CB SER L 94 " ideal model delta harmonic sigma weight residual 122.80 136.39 -13.59 0 2.50e+00 1.60e-01 2.95e+01 ... (remaining 3335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 685 0.125 - 0.251: 138 0.251 - 0.376: 18 0.376 - 0.501: 3 0.501 - 0.626: 1 Chirality restraints: 845 Sorted by residual: chirality pdb=" CA SER L 94 " pdb=" N SER L 94 " pdb=" C SER L 94 " pdb=" CB SER L 94 " both_signs ideal model delta sigma weight residual False 2.51 1.88 0.63 2.00e-01 2.50e+01 9.80e+00 chirality pdb=" CA PRO L 95 " pdb=" N PRO L 95 " pdb=" C PRO L 95 " pdb=" CB PRO L 95 " both_signs ideal model delta sigma weight residual False 2.72 2.28 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" CA PHE H 153 " pdb=" N PHE H 153 " pdb=" C PHE H 153 " pdb=" CB PHE H 153 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 842 not shown) Planarity restraints: 981 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL L 58 " 0.021 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C VAL L 58 " -0.069 2.00e-02 2.50e+03 pdb=" O VAL L 58 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO L 59 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 370 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.76e+00 pdb=" C ASN A 370 " -0.054 2.00e-02 2.50e+03 pdb=" O ASN A 370 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE A 371 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG L 61 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C ARG L 61 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG L 61 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE L 62 " -0.013 2.00e-02 2.50e+03 ... (remaining 978 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1603 2.81 - 3.33: 4610 3.33 - 3.85: 9274 3.85 - 4.38: 10677 4.38 - 4.90: 17516 Nonbonded interactions: 43680 Sorted by model distance: nonbonded pdb=" O SER A 366 " pdb=" ND2 ASN A 370 " model vdw 2.287 3.120 nonbonded pdb=" O SER A 408 " pdb=" NE2 GLN A 414 " model vdw 2.311 3.120 nonbonded pdb=" NE2 GLN L 148 " pdb=" O GLU L 196 " model vdw 2.338 3.120 nonbonded pdb=" OE1 GLU L 166 " pdb=" N GLN L 167 " model vdw 2.372 3.120 nonbonded pdb=" O PRO A 445 " pdb=" OG SER A 446 " model vdw 2.409 3.040 ... (remaining 43675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.610 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 5591 Z= 0.634 Angle : 1.488 11.501 7608 Z= 1.028 Chirality : 0.102 0.626 845 Planarity : 0.005 0.050 981 Dihedral : 18.676 83.063 2005 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 3.00 % Allowed : 17.14 % Favored : 79.86 % Rotamer: Outliers : 26.92 % Allowed : 11.91 % Favored : 61.17 % Cbeta Deviations : 1.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.71 (0.24), residues: 700 helix: -4.45 (0.50), residues: 25 sheet: -3.34 (0.33), residues: 174 loop : -4.26 (0.21), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 353 HIS 0.007 0.001 HIS H 35 PHE 0.035 0.003 PHE A 541 TYR 0.027 0.002 TYR H 152 ARG 0.006 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 179 time to evaluate : 0.608 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: 0.2214 time to fit residues: 78.7935 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 : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 8 PRO Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 49 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 118 ILE Chi-restraints excluded: chain L residue 124 GLU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 148 GLN Chi-restraints excluded: chain L residue 166 GLU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 97 ARG Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 136 LYS Chi-restraints excluded: chain H residue 159 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 591 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 58 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 27 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 0.0060 chunk 32 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 overall best weight: 0.2312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 3 GLN L 37 HIS L 89 GLN L 90 GLN L 101 GLN L 125 GLN L 148 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 207 HIS A 409 GLN A 414 GLN A 487 ASN A 544 ASN A 556 ASN A 563 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5591 Z= 0.219 Angle : 0.735 8.281 7608 Z= 0.381 Chirality : 0.048 0.254 845 Planarity : 0.006 0.057 981 Dihedral : 14.576 88.186 942 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.29 % Favored : 87.29 % Rotamer: Outliers : 14.03 % Allowed : 19.58 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.09 (0.26), residues: 700 helix: -4.01 (0.65), residues: 26 sheet: -3.20 (0.32), residues: 183 loop : -3.67 (0.24), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 97 HIS 0.016 0.002 HIS L 190 PHE 0.023 0.002 PHE A 429 TYR 0.018 0.002 TYR L 141 ARG 0.008 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 152 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 42 LYS cc_start: 0.8081 (ttmm) cc_final: 0.7863 (mtpp) REVERT: L 46 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.7947 (mt) REVERT: L 63 SER cc_start: 0.7119 (OUTLIER) cc_final: 0.6767 (p) REVERT: L 85 THR cc_start: 0.7133 (OUTLIER) cc_final: 0.6857 (p) REVERT: L 99 PHE cc_start: 0.7796 (m-80) cc_final: 0.7460 (m-80) REVERT: L 177 SER cc_start: 0.8118 (t) cc_final: 0.7799 (p) REVERT: L 191 LYS cc_start: 0.6485 (mtmm) cc_final: 0.6006 (mtmm) REVERT: H 43 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.6185 (mmmm) REVERT: H 54 SER cc_start: 0.7077 (OUTLIER) cc_final: 0.6799 (p) REVERT: H 59 TYR cc_start: 0.7948 (m-80) cc_final: 0.7660 (m-80) REVERT: H 83 ASN cc_start: 0.6617 (m-40) cc_final: 0.6280 (m-40) REVERT: H 107 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6349 (m-80) REVERT: A 336 CYS cc_start: 0.5477 (OUTLIER) cc_final: 0.5083 (m) REVERT: A 350 VAL cc_start: 0.8073 (OUTLIER) cc_final: 0.7835 (t) REVERT: A 356 LYS cc_start: 0.7603 (OUTLIER) cc_final: 0.7282 (tmtp) REVERT: A 365 TYR cc_start: 0.7605 (m-80) cc_final: 0.7079 (m-80) REVERT: A 371 PHE cc_start: 0.6057 (t80) cc_final: 0.5818 (t80) REVERT: A 428 ASP cc_start: 0.6415 (t0) cc_final: 0.6165 (t0) REVERT: A 440 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7404 (mmmt) REVERT: A 442 ASP cc_start: 0.7189 (m-30) cc_final: 0.6803 (m-30) REVERT: A 461 LEU cc_start: 0.7871 (tp) cc_final: 0.7460 (mp) REVERT: A 511 VAL cc_start: 0.7930 (OUTLIER) cc_final: 0.7625 (t) REVERT: A 515 PHE cc_start: 0.6855 (m-80) cc_final: 0.6296 (m-80) REVERT: A 528 LYS cc_start: 0.6501 (OUTLIER) cc_final: 0.6269 (mtmt) outliers start: 86 outliers final: 41 residues processed: 209 average time/residue: 0.2212 time to fit residues: 56.6338 Evaluate side-chains 191 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 138 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 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 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 34 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 0.3980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 125 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6225 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 5591 Z= 0.332 Angle : 0.786 7.819 7608 Z= 0.405 Chirality : 0.050 0.236 845 Planarity : 0.006 0.053 981 Dihedral : 10.892 59.995 845 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.43 % Allowed : 13.43 % Favored : 86.14 % Rotamer: Outliers : 10.93 % Allowed : 24.14 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.74 (0.27), residues: 700 helix: -3.97 (0.60), residues: 38 sheet: -3.03 (0.30), residues: 214 loop : -3.29 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.013 0.002 HIS L 190 PHE 0.018 0.002 PHE L 83 TYR 0.018 0.002 TYR L 141 ARG 0.005 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 137 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 46 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8235 (tp) REVERT: L 63 SER cc_start: 0.7691 (OUTLIER) cc_final: 0.7161 (p) REVERT: L 81 GLU cc_start: 0.5357 (mp0) cc_final: 0.5082 (mp0) REVERT: L 85 THR cc_start: 0.7527 (m) cc_final: 0.7258 (t) REVERT: L 99 PHE cc_start: 0.7855 (m-80) cc_final: 0.7598 (m-80) REVERT: L 107 ILE cc_start: 0.6256 (OUTLIER) cc_final: 0.5963 (mp) REVERT: L 124 GLU cc_start: 0.7220 (pm20) cc_final: 0.6882 (pm20) REVERT: L 191 LYS cc_start: 0.6500 (mtmm) cc_final: 0.6012 (mtmm) REVERT: H 32 TYR cc_start: 0.7200 (OUTLIER) cc_final: 0.6370 (m-10) REVERT: H 92 MET cc_start: 0.7229 (tpp) cc_final: 0.6708 (tpp) REVERT: H 107 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: H 173 PHE cc_start: 0.7068 (m-80) cc_final: 0.6804 (m-80) REVERT: A 353 TRP cc_start: 0.8081 (p-90) cc_final: 0.7729 (p-90) REVERT: A 356 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7289 (tmtp) REVERT: A 365 TYR cc_start: 0.7793 (m-80) cc_final: 0.7482 (m-80) REVERT: A 386 LYS cc_start: 0.7785 (mttp) cc_final: 0.7575 (mttp) REVERT: A 428 ASP cc_start: 0.6418 (t0) cc_final: 0.6164 (t0) REVERT: A 439 ASN cc_start: 0.7690 (t0) cc_final: 0.7298 (t0) REVERT: A 440 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7457 (mmmt) REVERT: A 442 ASP cc_start: 0.7113 (m-30) cc_final: 0.6689 (m-30) REVERT: A 455 LEU cc_start: 0.7586 (mp) cc_final: 0.7371 (mp) REVERT: A 511 VAL cc_start: 0.7926 (OUTLIER) cc_final: 0.7719 (t) REVERT: A 515 PHE cc_start: 0.6607 (m-80) cc_final: 0.6255 (m-80) REVERT: A 533 LEU cc_start: 0.7436 (tp) cc_final: 0.7221 (tp) REVERT: A 535 LYS cc_start: 0.6765 (mtpp) cc_final: 0.6472 (mtmm) outliers start: 67 outliers final: 47 residues processed: 179 average time/residue: 0.2263 time to fit residues: 49.9165 Evaluate side-chains 182 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 190 HIS Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 356 LYS Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 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 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 32 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 0.2980 chunk 59 optimal weight: 0.0060 chunk 17 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN L 167 GLN ** L 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 437 ASN A 540 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6211 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5591 Z= 0.256 Angle : 0.716 8.019 7608 Z= 0.366 Chirality : 0.048 0.238 845 Planarity : 0.005 0.059 981 Dihedral : 9.711 59.004 824 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.71 % Favored : 88.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.28), residues: 700 helix: -3.66 (0.77), residues: 32 sheet: -2.83 (0.32), residues: 201 loop : -2.95 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 97 HIS 0.013 0.002 HIS L 190 PHE 0.019 0.002 PHE A 371 TYR 0.011 0.002 TYR L 141 ARG 0.004 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 136 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 46 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8226 (tp) REVERT: L 63 SER cc_start: 0.7497 (OUTLIER) cc_final: 0.7098 (p) REVERT: L 79 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.6681 (pm20) REVERT: L 82 ASP cc_start: 0.6241 (m-30) cc_final: 0.5895 (m-30) REVERT: L 85 THR cc_start: 0.7487 (m) cc_final: 0.7239 (p) REVERT: L 155 LEU cc_start: 0.0918 (OUTLIER) cc_final: 0.0524 (mt) REVERT: L 191 LYS cc_start: 0.6478 (mtmm) cc_final: 0.5769 (mtmm) REVERT: H 43 LYS cc_start: 0.6704 (OUTLIER) cc_final: 0.6233 (mmmm) REVERT: H 92 MET cc_start: 0.7232 (tpp) cc_final: 0.6746 (tpp) REVERT: H 107 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6532 (m-80) REVERT: H 171 HIS cc_start: 0.6309 (m-70) cc_final: 0.6096 (m90) REVERT: H 173 PHE cc_start: 0.7054 (m-80) cc_final: 0.6754 (m-80) REVERT: A 336 CYS cc_start: 0.5494 (OUTLIER) cc_final: 0.5280 (m) REVERT: A 350 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7867 (p) REVERT: A 353 TRP cc_start: 0.8108 (p-90) cc_final: 0.7811 (p-90) REVERT: A 355 ARG cc_start: 0.7521 (mmm160) cc_final: 0.7280 (mmm160) REVERT: A 356 LYS cc_start: 0.7637 (tmtp) cc_final: 0.7221 (tmtp) REVERT: A 365 TYR cc_start: 0.7770 (m-80) cc_final: 0.7491 (m-80) REVERT: A 386 LYS cc_start: 0.7753 (mttp) cc_final: 0.7479 (mttp) REVERT: A 428 ASP cc_start: 0.6436 (t0) cc_final: 0.6180 (t0) REVERT: A 433 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8079 (p) REVERT: A 439 ASN cc_start: 0.7710 (t0) cc_final: 0.7316 (t0) REVERT: A 440 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7424 (mmmt) REVERT: A 511 VAL cc_start: 0.7939 (OUTLIER) cc_final: 0.7726 (t) REVERT: A 515 PHE cc_start: 0.6625 (m-80) cc_final: 0.6344 (m-80) REVERT: A 533 LEU cc_start: 0.7187 (tp) cc_final: 0.6959 (tp) REVERT: A 535 LYS cc_start: 0.6731 (mtpp) cc_final: 0.6476 (mtmm) outliers start: 66 outliers final: 39 residues processed: 181 average time/residue: 0.2184 time to fit residues: 49.0777 Evaluate side-chains 179 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 129 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 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 176 VAL Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 0.0050 chunk 59 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.4554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6227 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5591 Z= 0.251 Angle : 0.706 8.697 7608 Z= 0.362 Chirality : 0.048 0.242 845 Planarity : 0.005 0.052 981 Dihedral : 9.033 58.686 818 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.86 % Favored : 87.71 % Rotamer: Outliers : 10.11 % Allowed : 25.29 % Favored : 64.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.29), residues: 700 helix: -3.60 (0.80), residues: 32 sheet: -2.73 (0.31), residues: 217 loop : -2.81 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 436 HIS 0.007 0.001 HIS L 190 PHE 0.017 0.002 PHE L 83 TYR 0.023 0.002 TYR A 453 ARG 0.010 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 133 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: L 85 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.7289 (p) REVERT: L 155 LEU cc_start: 0.0830 (OUTLIER) cc_final: 0.0481 (mt) REVERT: H 13 GLN cc_start: 0.8548 (mt0) cc_final: 0.8290 (mt0) REVERT: H 43 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.6225 (mmmm) REVERT: H 48 VAL cc_start: 0.3567 (OUTLIER) cc_final: 0.2423 (t) REVERT: H 92 MET cc_start: 0.7248 (tpp) cc_final: 0.6751 (tpp) REVERT: H 107 TYR cc_start: 0.7415 (OUTLIER) cc_final: 0.6414 (m-80) REVERT: A 353 TRP cc_start: 0.8140 (p-90) cc_final: 0.7752 (p-90) REVERT: A 365 TYR cc_start: 0.7768 (m-80) cc_final: 0.7489 (m-80) REVERT: A 386 LYS cc_start: 0.7742 (mttp) cc_final: 0.7513 (mttp) REVERT: A 428 ASP cc_start: 0.6405 (t0) cc_final: 0.6141 (t0) REVERT: A 440 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7475 (mmmt) REVERT: A 455 LEU cc_start: 0.7365 (mp) cc_final: 0.7151 (mp) REVERT: A 466 ARG cc_start: 0.7462 (tpp80) cc_final: 0.7150 (mtp180) REVERT: A 515 PHE cc_start: 0.6637 (m-80) cc_final: 0.6345 (m-80) REVERT: A 535 LYS cc_start: 0.6805 (mtpp) cc_final: 0.6485 (mtpp) outliers start: 62 outliers final: 42 residues processed: 172 average time/residue: 0.2054 time to fit residues: 44.1902 Evaluate side-chains 177 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 215 ASP Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 414 GLN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 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 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 0.0970 chunk 22 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN A 437 ASN A 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5591 Z= 0.238 Angle : 0.694 9.818 7608 Z= 0.353 Chirality : 0.047 0.247 845 Planarity : 0.005 0.050 981 Dihedral : 8.692 58.452 813 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.43 % Favored : 89.14 % Rotamer: Outliers : 9.62 % Allowed : 26.75 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.29), residues: 700 helix: -3.11 (0.98), residues: 26 sheet: -2.64 (0.31), residues: 219 loop : -2.75 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.005 0.001 HIS H 35 PHE 0.018 0.002 PHE A 456 TYR 0.015 0.001 TYR A 453 ARG 0.009 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 144 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.7280 (p) REVERT: L 155 LEU cc_start: 0.0823 (OUTLIER) cc_final: 0.0507 (mt) REVERT: H 13 GLN cc_start: 0.8551 (mt0) cc_final: 0.8282 (mt0) REVERT: H 43 LYS cc_start: 0.6711 (OUTLIER) cc_final: 0.6219 (mmmm) REVERT: H 56 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6859 (p0) REVERT: H 60 LEU cc_start: 0.7324 (tp) cc_final: 0.6925 (tp) REVERT: H 92 MET cc_start: 0.7214 (tpp) cc_final: 0.6764 (tpp) REVERT: H 107 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.6456 (m-80) REVERT: H 149 VAL cc_start: 0.6604 (t) cc_final: 0.6366 (p) REVERT: A 353 TRP cc_start: 0.8180 (p-90) cc_final: 0.7893 (p-90) REVERT: A 355 ARG cc_start: 0.7436 (mmm160) cc_final: 0.7218 (mmm-85) REVERT: A 365 TYR cc_start: 0.7763 (m-80) cc_final: 0.7505 (m-80) REVERT: A 386 LYS cc_start: 0.7768 (mttp) cc_final: 0.7519 (mttp) REVERT: A 428 ASP cc_start: 0.6444 (t0) cc_final: 0.6166 (t0) REVERT: A 440 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7385 (mmmt) REVERT: A 515 PHE cc_start: 0.6658 (m-80) cc_final: 0.6446 (m-80) REVERT: A 535 LYS cc_start: 0.6748 (mtpp) cc_final: 0.6433 (mtpp) outliers start: 59 outliers final: 41 residues processed: 179 average time/residue: 0.2035 time to fit residues: 45.6228 Evaluate side-chains 188 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 110 ASP 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 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 0.0770 chunk 40 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 20 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 556 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5591 Z= 0.258 Angle : 0.729 10.106 7608 Z= 0.367 Chirality : 0.048 0.257 845 Planarity : 0.005 0.061 981 Dihedral : 8.488 58.476 812 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.43 % Allowed : 11.57 % Favored : 88.00 % Rotamer: Outliers : 9.46 % Allowed : 27.24 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.29), residues: 700 helix: -3.13 (0.97), residues: 26 sheet: -2.46 (0.31), residues: 229 loop : -2.68 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 97 HIS 0.005 0.001 HIS H 35 PHE 0.014 0.002 PHE L 83 TYR 0.011 0.001 TYR A 453 ARG 0.010 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 139 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7518 (OUTLIER) cc_final: 0.7297 (p) REVERT: L 107 ILE cc_start: 0.5671 (OUTLIER) cc_final: 0.5330 (mp) REVERT: L 155 LEU cc_start: 0.0830 (OUTLIER) cc_final: 0.0565 (mt) REVERT: L 177 SER cc_start: 0.8147 (t) cc_final: 0.7708 (p) REVERT: H 11 LEU cc_start: 0.8148 (tp) cc_final: 0.7928 (tt) REVERT: H 13 GLN cc_start: 0.8464 (mt0) cc_final: 0.8189 (mt0) REVERT: H 43 LYS cc_start: 0.6833 (OUTLIER) cc_final: 0.6286 (mmmm) REVERT: H 48 VAL cc_start: 0.3604 (OUTLIER) cc_final: 0.2491 (t) REVERT: H 56 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6926 (p0) REVERT: H 60 LEU cc_start: 0.7329 (tp) cc_final: 0.6936 (tp) REVERT: H 107 TYR cc_start: 0.7444 (OUTLIER) cc_final: 0.6415 (m-80) REVERT: H 149 VAL cc_start: 0.6636 (t) cc_final: 0.6390 (p) REVERT: A 353 TRP cc_start: 0.8247 (p-90) cc_final: 0.8037 (p-90) REVERT: A 356 LYS cc_start: 0.7545 (tmtp) cc_final: 0.7203 (tmtp) REVERT: A 386 LYS cc_start: 0.7794 (mttp) cc_final: 0.7541 (mttp) REVERT: A 428 ASP cc_start: 0.6406 (t0) cc_final: 0.6126 (t0) REVERT: A 440 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7381 (mmmt) REVERT: A 466 ARG cc_start: 0.7589 (tpp80) cc_final: 0.7288 (tpp80) REVERT: A 535 LYS cc_start: 0.6746 (mtpp) cc_final: 0.6401 (mtpp) outliers start: 58 outliers final: 40 residues processed: 175 average time/residue: 0.1989 time to fit residues: 43.8381 Evaluate side-chains 185 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 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 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 568 ASP 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 12 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 58 optimal weight: 50.0000 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 79 GLN A 321 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6294 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 5591 Z= 0.354 Angle : 0.785 12.214 7608 Z= 0.403 Chirality : 0.050 0.278 845 Planarity : 0.006 0.057 981 Dihedral : 8.633 59.457 810 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.29 % Allowed : 12.86 % Favored : 86.86 % Rotamer: Outliers : 8.65 % Allowed : 27.73 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.29), residues: 700 helix: -2.39 (1.25), residues: 20 sheet: -2.36 (0.32), residues: 227 loop : -2.62 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 97 HIS 0.006 0.002 HIS H 35 PHE 0.018 0.002 PHE A 456 TYR 0.019 0.002 TYR L 141 ARG 0.008 0.001 ARG A 454 *********************** 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 199 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 146 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 79 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.7056 (pm20) REVERT: L 85 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7290 (p) REVERT: L 155 LEU cc_start: 0.0781 (OUTLIER) cc_final: 0.0534 (mt) REVERT: L 177 SER cc_start: 0.8122 (t) cc_final: 0.7700 (p) REVERT: H 13 GLN cc_start: 0.8456 (mt0) cc_final: 0.8206 (mt0) REVERT: H 43 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6357 (mmmm) REVERT: H 48 VAL cc_start: 0.3872 (OUTLIER) cc_final: 0.2685 (t) REVERT: H 56 ASP cc_start: 0.7331 (p0) cc_final: 0.7130 (p0) REVERT: H 60 LEU cc_start: 0.7315 (tp) cc_final: 0.7013 (tp) REVERT: H 107 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6371 (m-80) REVERT: H 149 VAL cc_start: 0.6685 (t) cc_final: 0.6419 (p) REVERT: A 355 ARG cc_start: 0.7475 (mmm160) cc_final: 0.7223 (mmm160) REVERT: A 356 LYS cc_start: 0.7531 (tmtp) cc_final: 0.7151 (tmtp) REVERT: A 386 LYS cc_start: 0.7878 (mttp) cc_final: 0.7666 (mttp) REVERT: A 428 ASP cc_start: 0.6441 (t0) cc_final: 0.6165 (t0) REVERT: A 439 ASN cc_start: 0.7446 (t0) cc_final: 0.7155 (t0) REVERT: A 466 ARG cc_start: 0.7762 (tpp80) cc_final: 0.7452 (tpp80) REVERT: A 535 LYS cc_start: 0.6757 (mtpp) cc_final: 0.6547 (ttmm) outliers start: 53 outliers final: 41 residues processed: 178 average time/residue: 0.2076 time to fit residues: 45.7701 Evaluate side-chains 188 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 141 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 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 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE 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 26 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 5591 Z= 0.302 Angle : 0.782 11.348 7608 Z= 0.394 Chirality : 0.050 0.260 845 Planarity : 0.006 0.058 981 Dihedral : 8.281 59.575 804 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.14 % Favored : 88.57 % Rotamer: Outliers : 7.83 % Allowed : 30.18 % Favored : 61.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.30), residues: 700 helix: -3.09 (0.99), residues: 26 sheet: -2.32 (0.32), residues: 230 loop : -2.53 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 97 HIS 0.006 0.001 HIS H 35 PHE 0.019 0.002 PHE A 456 TYR 0.013 0.002 TYR L 141 ARG 0.013 0.001 ARG H 3 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7541 (OUTLIER) cc_final: 0.7304 (p) REVERT: L 155 LEU cc_start: 0.0774 (OUTLIER) cc_final: 0.0543 (mt) REVERT: L 177 SER cc_start: 0.8164 (t) cc_final: 0.7750 (p) REVERT: H 43 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6666 (mmmm) REVERT: H 48 VAL cc_start: 0.3907 (OUTLIER) cc_final: 0.2756 (t) REVERT: H 60 LEU cc_start: 0.7228 (tp) cc_final: 0.6913 (tp) REVERT: H 107 TYR cc_start: 0.7504 (OUTLIER) cc_final: 0.6362 (m-80) REVERT: H 149 VAL cc_start: 0.6712 (t) cc_final: 0.6424 (m) REVERT: A 347 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6268 (m-80) REVERT: A 355 ARG cc_start: 0.7408 (mmm160) cc_final: 0.7116 (mmm-85) REVERT: A 356 LYS cc_start: 0.7551 (tmtp) cc_final: 0.7181 (tmtp) REVERT: A 386 LYS cc_start: 0.7801 (mttp) cc_final: 0.7522 (mttp) REVERT: A 428 ASP cc_start: 0.6415 (t0) cc_final: 0.6137 (t0) REVERT: A 439 ASN cc_start: 0.7600 (t0) cc_final: 0.7209 (t0) REVERT: A 440 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7697 (mmmt) REVERT: A 466 ARG cc_start: 0.7867 (tpp80) cc_final: 0.7511 (tpp80) REVERT: A 535 LYS cc_start: 0.6668 (mtpp) cc_final: 0.6330 (mtpp) REVERT: A 576 VAL cc_start: 0.7793 (t) cc_final: 0.7573 (m) outliers start: 48 outliers final: 39 residues processed: 172 average time/residue: 0.2125 time to fit residues: 45.4468 Evaluate side-chains 185 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 155 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 chunk 43 optimal weight: 0.4980 chunk 58 optimal weight: 0.0970 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.6031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 5591 Z= 0.236 Angle : 0.727 10.225 7608 Z= 0.369 Chirality : 0.048 0.232 845 Planarity : 0.006 0.056 981 Dihedral : 7.933 58.646 801 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.57 % Favored : 90.14 % Rotamer: Outliers : 7.01 % Allowed : 30.51 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.30), residues: 700 helix: -3.11 (0.98), residues: 26 sheet: -2.18 (0.33), residues: 230 loop : -2.45 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 97 HIS 0.005 0.001 HIS H 35 PHE 0.018 0.002 PHE A 456 TYR 0.011 0.001 TYR L 141 ARG 0.012 0.001 ARG H 3 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 85 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7254 (p) REVERT: L 177 SER cc_start: 0.8172 (t) cc_final: 0.7776 (p) REVERT: H 13 GLN cc_start: 0.8445 (mt0) cc_final: 0.8190 (mt0) REVERT: H 43 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6649 (mmmm) REVERT: H 48 VAL cc_start: 0.3802 (OUTLIER) cc_final: 0.2489 (t) REVERT: H 51 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8587 (p) REVERT: H 60 LEU cc_start: 0.7206 (tp) cc_final: 0.6694 (tp) REVERT: H 63 VAL cc_start: 0.7592 (t) cc_final: 0.7332 (p) REVERT: H 107 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.6429 (m-80) REVERT: H 149 VAL cc_start: 0.6725 (t) cc_final: 0.6474 (m) REVERT: A 356 LYS cc_start: 0.7542 (tmtp) cc_final: 0.7155 (tmtp) REVERT: A 382 VAL cc_start: 0.8398 (t) cc_final: 0.7954 (p) REVERT: A 386 LYS cc_start: 0.7758 (mttp) cc_final: 0.7477 (mttp) REVERT: A 428 ASP cc_start: 0.6357 (t0) cc_final: 0.6136 (t0) REVERT: A 466 ARG cc_start: 0.7826 (tpp80) cc_final: 0.7527 (tpp80) REVERT: A 513 LEU cc_start: 0.7557 (mt) cc_final: 0.7318 (mt) REVERT: A 576 VAL cc_start: 0.7768 (t) cc_final: 0.7534 (m) outliers start: 43 outliers final: 34 residues processed: 178 average time/residue: 0.2123 time to fit residues: 46.7811 Evaluate side-chains 187 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 148 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 35 TRP Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 85 THR Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 107 TYR Chi-restraints excluded: chain H residue 110 ASP Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 216 LYS Chi-restraints excluded: chain H residue 218 VAL Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 457 ARG Chi-restraints excluded: chain A residue 460 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 56 optimal weight: 0.0570 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.174701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.151558 restraints weight = 9200.443| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.24 r_work: 0.3833 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 5591 Z= 0.259 Angle : 0.756 10.802 7608 Z= 0.381 Chirality : 0.049 0.235 845 Planarity : 0.006 0.063 981 Dihedral : 7.909 58.909 799 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.29 % Allowed : 11.00 % Favored : 88.71 % Rotamer: Outliers : 6.36 % Allowed : 31.00 % Favored : 62.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.30), residues: 700 helix: -3.10 (0.98), residues: 26 sheet: -2.15 (0.33), residues: 232 loop : -2.38 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 112 HIS 0.005 0.001 HIS H 35 PHE 0.024 0.002 PHE A 565 TYR 0.012 0.002 TYR L 141 ARG 0.013 0.001 ARG H 3 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.07 seconds wall clock time: 35 minutes 12.56 seconds (2112.56 seconds total)