Starting phenix.real_space_refine on Thu Nov 14 07:34:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdt_37145/11_2024/8kdt_37145.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdt_37145/11_2024/8kdt_37145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdt_37145/11_2024/8kdt_37145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdt_37145/11_2024/8kdt_37145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdt_37145/11_2024/8kdt_37145.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kdt_37145/11_2024/8kdt_37145.cif" } resolution = 3.04 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= 0.023 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 22 5.16 5 C 3075 2.51 5 N 803 2.21 5 O 937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4837 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1546 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 14, 'TRANS': 179} Chain: "H" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1638 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "L" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1653 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 12, 'TRANS': 200} Time building chain proxies: 3.82, per 1000 atoms: 0.79 Number of scatterers: 4837 At special positions: 0 Unit cell: (72.696, 106.248, 103.452, 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 22 16.00 O 937 8.00 N 803 7.00 C 3075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 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: 1.17 Conformation dependent library (CDL) restraints added in 616.2 milliseconds 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1166 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 11 sheets defined 5.3% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.743A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 376 removed outlier: 3.698A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.843A pdb=" N THR H 138 " --> pdb=" O SER H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 196 Processing helix chain 'L' and resid 123 through 128 removed outlier: 3.613A pdb=" N LEU L 127 " --> pdb=" O SER L 123 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS L 128 " --> pdb=" O ASP L 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 123 through 128' Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.806A pdb=" N GLU L 189 " --> pdb=" O LYS L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 removed outlier: 3.691A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 498 " --> pdb=" O ASP A 385 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A 494 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 422 " --> pdb=" O THR A 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.590A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.825A pdb=" N THR H 119 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AA6, first strand: chain 'H' and resid 172 through 177 removed outlier: 5.281A pdb=" N SER H 186 " --> pdb=" O PRO H 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.621A pdb=" N TYR L 86 " --> pdb=" O THR L 104 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 21 through 23 removed outlier: 3.665A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.462A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 120 removed outlier: 3.600A pdb=" N VAL L 135 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 146 through 152 removed outlier: 3.956A pdb=" N ALA L 195 " --> pdb=" O LYS L 151 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 240 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: 1.18 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1525 1.34 - 1.46: 1238 1.46 - 1.58: 2174 1.58 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 4965 Sorted by residual: bond pdb=" C PRO A 469 " pdb=" N PRO A 470 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 bond pdb=" C TRP L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.50e-01 bond pdb=" CA VAL L 152 " pdb=" CB VAL L 152 " ideal model delta sigma weight residual 1.527 1.539 -0.012 1.31e-02 5.83e+03 8.88e-01 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.70e-01 bond pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " ideal model delta sigma weight residual 1.532 1.549 -0.016 2.01e-02 2.48e+03 6.57e-01 ... (remaining 4960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 6540 1.21 - 2.42: 172 2.42 - 3.63: 41 3.63 - 4.84: 7 4.84 - 6.05: 6 Bond angle restraints: 6766 Sorted by residual: angle pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 113.60 119.10 -5.50 1.90e+00 2.77e-01 8.38e+00 angle pdb=" N VAL H 120 " pdb=" CA VAL H 120 " pdb=" C VAL H 120 " ideal model delta sigma weight residual 106.61 110.59 -3.98 1.78e+00 3.16e-01 5.00e+00 angle pdb=" C ASP H 54 " pdb=" N ALA H 55 " pdb=" CA ALA H 55 " ideal model delta sigma weight residual 122.17 118.73 3.44 1.54e+00 4.22e-01 4.98e+00 angle pdb=" N GLU H 155 " pdb=" CA GLU H 155 " pdb=" C GLU H 155 " ideal model delta sigma weight residual 109.81 114.49 -4.68 2.21e+00 2.05e-01 4.49e+00 angle pdb=" C LEU A 448 " pdb=" N ARG A 449 " pdb=" CA ARG A 449 " ideal model delta sigma weight residual 122.71 128.72 -6.01 3.03e+00 1.09e-01 3.94e+00 ... (remaining 6761 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.32: 2697 10.32 - 20.63: 168 20.63 - 30.95: 69 30.95 - 41.26: 16 41.26 - 51.58: 8 Dihedral angle restraints: 2958 sinusoidal: 1134 harmonic: 1824 Sorted by residual: dihedral pdb=" CA GLU H 46 " pdb=" C GLU H 46 " pdb=" N TRP H 47 " pdb=" CA TRP H 47 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLU H 155 " pdb=" C GLU H 155 " pdb=" N PRO H 156 " pdb=" CA PRO H 156 " ideal model delta harmonic sigma weight residual 180.00 157.23 22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ARG H 38 " pdb=" CB ARG H 38 " pdb=" CG ARG H 38 " pdb=" CD ARG H 38 " ideal model delta sinusoidal sigma weight residual -60.00 -111.58 51.58 3 1.50e+01 4.44e-03 9.03e+00 ... (remaining 2955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 426 0.025 - 0.050: 192 0.050 - 0.076: 68 0.076 - 0.101: 46 0.101 - 0.126: 18 Chirality restraints: 750 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA ILE L 58 " pdb=" N ILE L 58 " pdb=" C ILE L 58 " pdb=" CB ILE L 58 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 chirality pdb=" CA ILE A 397 " pdb=" N ILE A 397 " pdb=" C ILE A 397 " pdb=" CB ILE A 397 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.24e-01 ... (remaining 747 not shown) Planarity restraints: 867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 14 " -0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO L 15 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS H 13 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.92e+00 pdb=" N PRO H 14 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.011 2.00e-02 2.50e+03 8.65e-03 1.87e+00 pdb=" CG TRP H 47 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.002 2.00e-02 2.50e+03 ... (remaining 864 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 814 2.77 - 3.30: 4271 3.30 - 3.84: 7761 3.84 - 4.37: 8839 4.37 - 4.90: 15418 Nonbonded interactions: 37103 Sorted by model distance: nonbonded pdb=" OG SER A 380 " pdb=" O GLU A 502 " model vdw 2.240 3.040 nonbonded pdb=" OH TYR A 436 " pdb=" OH TYR A 484 " model vdw 2.285 3.040 nonbonded pdb=" OD1 ASP L 172 " pdb=" OG1 THR L 174 " model vdw 2.291 3.040 nonbonded pdb=" O ALA H 106 " pdb=" NH1 ARG L 91 " model vdw 2.294 3.120 nonbonded pdb=" OD2 ASP A 429 " pdb=" OH TYR A 438 " model vdw 2.299 3.040 ... (remaining 37098 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: 1.820 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: 15.710 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 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 : 0.002 0.026 4965 Z= 0.119 Angle : 0.515 6.049 6766 Z= 0.283 Chirality : 0.039 0.126 750 Planarity : 0.004 0.037 867 Dihedral : 8.532 51.579 1768 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 5.91 % Allowed : 5.73 % Favored : 88.35 % 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: -4.43 (0.29), residues: 619 helix: -5.41 (0.31), residues: 6 sheet: -2.84 (0.30), residues: 217 loop : -3.10 (0.27), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 47 HIS 0.001 0.000 HIS L 90 PHE 0.009 0.001 PHE A 360 TYR 0.006 0.001 TYR L 49 ARG 0.001 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: A 447 LYS cc_start: 0.7994 (mttm) cc_final: 0.7772 (mttm) REVERT: A 473 ASN cc_start: 0.7536 (m-40) cc_final: 0.7310 (m-40) REVERT: A 510 VAL cc_start: 0.7269 (OUTLIER) cc_final: 0.6959 (m) REVERT: H 57 SER cc_start: 0.7623 (m) cc_final: 0.7358 (t) REVERT: H 78 THR cc_start: 0.8431 (m) cc_final: 0.7930 (p) REVERT: H 145 LEU cc_start: 0.8025 (mt) cc_final: 0.7631 (mt) REVERT: H 187 SER cc_start: 0.7639 (t) cc_final: 0.7385 (m) REVERT: H 216 LYS cc_start: 0.8452 (tppt) cc_final: 0.8204 (tppp) REVERT: L 18 ARG cc_start: 0.7356 (ptm-80) cc_final: 0.7110 (ptm-80) outliers start: 32 outliers final: 14 residues processed: 194 average time/residue: 0.1293 time to fit residues: 33.7636 Evaluate side-chains 174 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 411 LYS Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 32 HIS Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 171 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 473 ASN H 32 HIS H 178 GLN L 37 GLN L 89 GLN L 102 GLN ** L 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4965 Z= 0.243 Angle : 0.631 6.998 6766 Z= 0.319 Chirality : 0.046 0.184 750 Planarity : 0.005 0.041 867 Dihedral : 6.397 48.454 708 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 6.65 % Allowed : 13.49 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.32), residues: 619 helix: -5.39 (0.31), residues: 6 sheet: -1.90 (0.34), residues: 222 loop : -2.76 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.005 0.001 HIS L 90 PHE 0.014 0.002 PHE A 360 TYR 0.024 0.002 TYR A 442 ARG 0.002 0.000 ARG L 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 161 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 PHE cc_start: 0.6223 (OUTLIER) cc_final: 0.5552 (p90) REVERT: A 447 LYS cc_start: 0.7986 (mttm) cc_final: 0.7693 (mttm) REVERT: H 36 TRP cc_start: 0.7585 (m100) cc_final: 0.7330 (m100) REVERT: H 69 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.7973 (p) REVERT: H 71 THR cc_start: 0.8269 (t) cc_final: 0.7978 (p) REVERT: H 145 LEU cc_start: 0.8208 (mt) cc_final: 0.7862 (mt) REVERT: H 187 SER cc_start: 0.7808 (t) cc_final: 0.7509 (m) REVERT: H 216 LYS cc_start: 0.8559 (tppt) cc_final: 0.8283 (tppp) REVERT: H 217 LYS cc_start: 0.8449 (tttt) cc_final: 0.8155 (tttt) REVERT: L 18 ARG cc_start: 0.7387 (ptm-80) cc_final: 0.7153 (ptm-80) REVERT: L 22 SER cc_start: 0.8196 (p) cc_final: 0.7852 (m) REVERT: L 46 LEU cc_start: 0.7546 (tp) cc_final: 0.7327 (tp) REVERT: L 138 LEU cc_start: 0.7348 (mm) cc_final: 0.7126 (mp) REVERT: L 157 GLN cc_start: 0.7359 (tp40) cc_final: 0.7031 (tp40) REVERT: L 162 GLN cc_start: 0.8416 (mt0) cc_final: 0.8185 (mt0) REVERT: L 164 SER cc_start: 0.8580 (t) cc_final: 0.7982 (p) REVERT: L 172 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6958 (p0) outliers start: 36 outliers final: 22 residues processed: 186 average time/residue: 0.1382 time to fit residues: 34.0300 Evaluate side-chains 182 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 184 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.0170 chunk 18 optimal weight: 3.9990 chunk 44 optimal weight: 0.0270 chunk 54 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 ASN L 38 GLN L 160 ASN L 191 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 4965 Z= 0.199 Angle : 0.609 8.824 6766 Z= 0.304 Chirality : 0.045 0.248 750 Planarity : 0.005 0.039 867 Dihedral : 6.150 48.928 701 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.55 % Allowed : 18.67 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -3.16 (0.33), residues: 619 helix: -5.38 (0.31), residues: 6 sheet: -1.43 (0.36), residues: 214 loop : -2.57 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.015 0.002 PHE A 379 TYR 0.029 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 LYS cc_start: 0.7966 (mttm) cc_final: 0.7672 (mttm) REVERT: H 36 TRP cc_start: 0.7585 (m100) cc_final: 0.7321 (m100) REVERT: H 69 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8008 (p) REVERT: H 71 THR cc_start: 0.8207 (t) cc_final: 0.7912 (p) REVERT: H 91 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7854 (p) REVERT: H 145 LEU cc_start: 0.8181 (mt) cc_final: 0.7839 (mt) REVERT: H 187 SER cc_start: 0.7913 (t) cc_final: 0.7567 (m) REVERT: H 188 VAL cc_start: 0.8390 (t) cc_final: 0.8108 (p) REVERT: H 216 LYS cc_start: 0.8569 (tppt) cc_final: 0.8302 (tppp) REVERT: H 217 LYS cc_start: 0.8435 (tttt) cc_final: 0.8148 (tttt) REVERT: L 18 ARG cc_start: 0.7334 (ptm-80) cc_final: 0.7107 (ptm-80) REVERT: L 22 SER cc_start: 0.8189 (p) cc_final: 0.7860 (m) REVERT: L 162 GLN cc_start: 0.8426 (mt0) cc_final: 0.8211 (mt0) REVERT: L 164 SER cc_start: 0.8608 (t) cc_final: 0.8060 (p) REVERT: L 172 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6901 (p0) REVERT: L 175 TYR cc_start: 0.7874 (m-80) cc_final: 0.7128 (m-80) outliers start: 30 outliers final: 22 residues processed: 178 average time/residue: 0.1362 time to fit residues: 32.6586 Evaluate side-chains 181 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 184 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.0470 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 ASN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4965 Z= 0.217 Angle : 0.619 10.759 6766 Z= 0.308 Chirality : 0.045 0.256 750 Planarity : 0.005 0.038 867 Dihedral : 6.333 49.006 701 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 6.10 % Allowed : 19.78 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.92 (0.33), residues: 619 helix: -5.38 (0.30), residues: 6 sheet: -1.33 (0.35), residues: 219 loop : -2.35 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.026 0.002 PHE A 460 TYR 0.031 0.002 TYR A 442 ARG 0.002 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ILE cc_start: 0.8865 (mt) cc_final: 0.8629 (mt) REVERT: A 447 LYS cc_start: 0.8001 (mttm) cc_final: 0.7707 (mttm) REVERT: A 457 ASN cc_start: 0.8084 (t0) cc_final: 0.7848 (t0) REVERT: H 36 TRP cc_start: 0.7595 (m100) cc_final: 0.7323 (m100) REVERT: H 69 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8037 (p) REVERT: H 71 THR cc_start: 0.8200 (t) cc_final: 0.7925 (p) REVERT: H 90 ASP cc_start: 0.8056 (m-30) cc_final: 0.7805 (t0) REVERT: H 91 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7907 (p) REVERT: H 145 LEU cc_start: 0.8267 (mt) cc_final: 0.7985 (mt) REVERT: H 187 SER cc_start: 0.8045 (t) cc_final: 0.7829 (t) REVERT: H 188 VAL cc_start: 0.8376 (t) cc_final: 0.8037 (p) REVERT: H 216 LYS cc_start: 0.8607 (tppt) cc_final: 0.8335 (tppp) REVERT: H 217 LYS cc_start: 0.8434 (tttt) cc_final: 0.8140 (tttt) REVERT: L 18 ARG cc_start: 0.7340 (ptm-80) cc_final: 0.7136 (ptm-80) REVERT: L 22 SER cc_start: 0.8210 (p) cc_final: 0.7913 (m) REVERT: L 164 SER cc_start: 0.8601 (t) cc_final: 0.8151 (p) REVERT: L 172 ASP cc_start: 0.7169 (OUTLIER) cc_final: 0.6869 (p0) REVERT: L 175 TYR cc_start: 0.7972 (m-80) cc_final: 0.7337 (m-80) outliers start: 33 outliers final: 23 residues processed: 177 average time/residue: 0.1376 time to fit residues: 32.8146 Evaluate side-chains 182 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 127 SER Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 chunk 24 optimal weight: 0.0070 chunk 50 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 52 optimal weight: 0.0040 chunk 14 optimal weight: 0.0270 chunk 19 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.2670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4965 Z= 0.165 Angle : 0.618 9.421 6766 Z= 0.301 Chirality : 0.045 0.270 750 Planarity : 0.005 0.040 867 Dihedral : 6.270 49.403 701 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.25 % Allowed : 22.18 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.78 (0.33), residues: 619 helix: -5.37 (0.30), residues: 6 sheet: -1.34 (0.33), residues: 230 loop : -2.20 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.024 0.002 PHE A 460 TYR 0.029 0.001 TYR A 442 ARG 0.002 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LYS cc_start: 0.7908 (mttm) cc_final: 0.7597 (mttm) REVERT: A 457 ASN cc_start: 0.8116 (t0) cc_final: 0.7892 (t0) REVERT: A 501 PHE cc_start: 0.7346 (m-80) cc_final: 0.7081 (m-80) REVERT: H 36 TRP cc_start: 0.7603 (m100) cc_final: 0.7323 (m100) REVERT: H 69 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8043 (p) REVERT: H 71 THR cc_start: 0.8173 (t) cc_final: 0.7913 (p) REVERT: H 90 ASP cc_start: 0.7999 (m-30) cc_final: 0.7762 (t0) REVERT: H 91 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7857 (p) REVERT: H 114 GLN cc_start: 0.8056 (pm20) cc_final: 0.7783 (pm20) REVERT: H 145 LEU cc_start: 0.8228 (mt) cc_final: 0.7937 (mt) REVERT: H 216 LYS cc_start: 0.8555 (tppt) cc_final: 0.8283 (tppp) REVERT: H 217 LYS cc_start: 0.8423 (tttt) cc_final: 0.8149 (tttt) REVERT: L 22 SER cc_start: 0.8195 (p) cc_final: 0.7890 (m) REVERT: L 164 SER cc_start: 0.8575 (t) cc_final: 0.8104 (p) REVERT: L 172 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6829 (p0) REVERT: L 175 TYR cc_start: 0.7953 (m-80) cc_final: 0.7356 (m-80) outliers start: 23 outliers final: 17 residues processed: 170 average time/residue: 0.1334 time to fit residues: 30.6353 Evaluate side-chains 173 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 0.0040 chunk 59 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 4965 Z= 0.210 Angle : 0.627 10.589 6766 Z= 0.310 Chirality : 0.045 0.264 750 Planarity : 0.005 0.036 867 Dihedral : 6.346 49.983 700 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 5.91 % Allowed : 20.89 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.67 (0.33), residues: 619 helix: -5.03 (0.30), residues: 12 sheet: -0.98 (0.34), residues: 221 loop : -2.26 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.026 0.002 PHE A 460 TYR 0.031 0.001 TYR A 442 ARG 0.002 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 447 LYS cc_start: 0.7944 (mttm) cc_final: 0.7640 (mttm) REVERT: A 457 ASN cc_start: 0.8112 (t0) cc_final: 0.7795 (t0) REVERT: A 501 PHE cc_start: 0.7516 (m-80) cc_final: 0.7233 (m-80) REVERT: H 36 TRP cc_start: 0.7587 (m100) cc_final: 0.7348 (m100) REVERT: H 69 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8065 (p) REVERT: H 71 THR cc_start: 0.8181 (t) cc_final: 0.7938 (p) REVERT: H 90 ASP cc_start: 0.8060 (m-30) cc_final: 0.7813 (t0) REVERT: H 91 THR cc_start: 0.8164 (OUTLIER) cc_final: 0.7915 (p) REVERT: H 114 GLN cc_start: 0.8096 (pm20) cc_final: 0.7723 (pm20) REVERT: H 145 LEU cc_start: 0.8199 (mt) cc_final: 0.7868 (mt) REVERT: H 216 LYS cc_start: 0.8606 (tppt) cc_final: 0.8328 (tppp) REVERT: H 217 LYS cc_start: 0.8425 (tttt) cc_final: 0.8135 (tttt) REVERT: L 22 SER cc_start: 0.8225 (p) cc_final: 0.7926 (m) REVERT: L 67 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7941 (p) REVERT: L 138 LEU cc_start: 0.7398 (mt) cc_final: 0.7172 (mm) REVERT: L 164 SER cc_start: 0.8566 (t) cc_final: 0.8045 (p) REVERT: L 172 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6751 (p0) REVERT: L 173 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8158 (p) REVERT: L 175 TYR cc_start: 0.8059 (m-80) cc_final: 0.7570 (m-80) outliers start: 32 outliers final: 23 residues processed: 173 average time/residue: 0.1403 time to fit residues: 32.5651 Evaluate side-chains 181 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.0980 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.0670 chunk 27 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4965 Z= 0.172 Angle : 0.614 11.571 6766 Z= 0.302 Chirality : 0.044 0.255 750 Planarity : 0.005 0.038 867 Dihedral : 6.329 50.435 700 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 5.73 % Allowed : 22.18 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.50 (0.34), residues: 619 helix: -4.74 (0.60), residues: 12 sheet: -0.83 (0.35), residues: 221 loop : -2.16 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.027 0.002 PHE A 416 TYR 0.031 0.001 TYR A 442 ARG 0.002 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 ILE cc_start: 0.8854 (mt) cc_final: 0.8596 (mt) REVERT: A 447 LYS cc_start: 0.7903 (mttm) cc_final: 0.7649 (mttm) REVERT: A 457 ASN cc_start: 0.8145 (t0) cc_final: 0.7813 (t0) REVERT: A 501 PHE cc_start: 0.7527 (m-80) cc_final: 0.7218 (m-80) REVERT: H 36 TRP cc_start: 0.7575 (m100) cc_final: 0.7332 (m100) REVERT: H 69 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8077 (p) REVERT: H 71 THR cc_start: 0.8162 (t) cc_final: 0.7920 (p) REVERT: H 90 ASP cc_start: 0.8010 (m-30) cc_final: 0.7754 (t0) REVERT: H 91 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7892 (p) REVERT: H 114 GLN cc_start: 0.8038 (pm20) cc_final: 0.7701 (pm20) REVERT: H 145 LEU cc_start: 0.8265 (mt) cc_final: 0.7899 (mt) REVERT: H 216 LYS cc_start: 0.8578 (tppt) cc_final: 0.8306 (tppp) REVERT: H 217 LYS cc_start: 0.8413 (tttt) cc_final: 0.8140 (tttt) REVERT: L 22 SER cc_start: 0.8202 (p) cc_final: 0.7896 (m) REVERT: L 164 SER cc_start: 0.8561 (t) cc_final: 0.8043 (p) REVERT: L 172 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6821 (p0) REVERT: L 175 TYR cc_start: 0.8066 (m-80) cc_final: 0.7595 (m-80) outliers start: 31 outliers final: 23 residues processed: 172 average time/residue: 0.1352 time to fit residues: 31.0265 Evaluate side-chains 178 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 117 LEU Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 4965 Z= 0.308 Angle : 0.689 12.769 6766 Z= 0.345 Chirality : 0.046 0.278 750 Planarity : 0.005 0.038 867 Dihedral : 6.745 52.720 700 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.47 % Favored : 88.53 % Rotamer: Outliers : 6.10 % Allowed : 22.18 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.44 (0.34), residues: 619 helix: -4.55 (0.82), residues: 12 sheet: -0.88 (0.35), residues: 222 loop : -2.07 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 47 HIS 0.004 0.001 HIS H 32 PHE 0.026 0.003 PHE A 460 TYR 0.033 0.002 TYR A 442 ARG 0.002 0.001 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.6974 (m-10) REVERT: A 360 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5680 (p90) REVERT: A 379 PHE cc_start: 0.7205 (m-80) cc_final: 0.6978 (m-10) REVERT: A 428 ILE cc_start: 0.8896 (mt) cc_final: 0.8631 (mt) REVERT: A 436 TYR cc_start: 0.7979 (m-80) cc_final: 0.7741 (m-80) REVERT: A 447 LYS cc_start: 0.8007 (mttm) cc_final: 0.7715 (mttm) REVERT: A 457 ASN cc_start: 0.8102 (t0) cc_final: 0.7723 (t0) REVERT: H 36 TRP cc_start: 0.7615 (m100) cc_final: 0.7378 (m100) REVERT: H 69 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8073 (p) REVERT: H 71 THR cc_start: 0.8173 (t) cc_final: 0.7945 (p) REVERT: H 90 ASP cc_start: 0.8081 (m-30) cc_final: 0.7824 (t0) REVERT: H 114 GLN cc_start: 0.8144 (pm20) cc_final: 0.7745 (pm20) REVERT: H 145 LEU cc_start: 0.8317 (mt) cc_final: 0.7961 (mt) REVERT: H 216 LYS cc_start: 0.8633 (tppt) cc_final: 0.8360 (tppp) REVERT: H 217 LYS cc_start: 0.8415 (tttt) cc_final: 0.8139 (tttt) REVERT: L 22 SER cc_start: 0.8225 (p) cc_final: 0.7915 (m) REVERT: L 89 GLN cc_start: 0.7965 (tt0) cc_final: 0.7702 (tt0) REVERT: L 164 SER cc_start: 0.8569 (t) cc_final: 0.8005 (p) REVERT: L 172 ASP cc_start: 0.7116 (OUTLIER) cc_final: 0.6860 (p0) REVERT: L 173 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8300 (p) REVERT: L 175 TYR cc_start: 0.8200 (m-80) cc_final: 0.7852 (m-80) REVERT: L 201 GLN cc_start: 0.8078 (tt0) cc_final: 0.7825 (tt0) outliers start: 33 outliers final: 23 residues processed: 175 average time/residue: 0.1416 time to fit residues: 33.1647 Evaluate side-chains 180 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 360 PHE Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 172 ASP Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 194 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 157 GLN L 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 4965 Z= 0.271 Angle : 0.681 13.004 6766 Z= 0.340 Chirality : 0.046 0.275 750 Planarity : 0.005 0.040 867 Dihedral : 6.677 53.300 698 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 5.36 % Allowed : 24.03 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.41 (0.34), residues: 619 helix: -4.38 (1.01), residues: 12 sheet: -0.92 (0.35), residues: 222 loop : -2.00 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.030 0.003 PHE A 416 TYR 0.033 0.002 TYR A 442 ARG 0.003 0.000 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6996 (m-10) REVERT: A 379 PHE cc_start: 0.7184 (m-80) cc_final: 0.6942 (m-10) REVERT: A 436 TYR cc_start: 0.7982 (m-80) cc_final: 0.7705 (m-80) REVERT: A 447 LYS cc_start: 0.8035 (mttm) cc_final: 0.7720 (mttm) REVERT: A 457 ASN cc_start: 0.8156 (t0) cc_final: 0.7746 (t0) REVERT: H 36 TRP cc_start: 0.7643 (m100) cc_final: 0.7391 (m100) REVERT: H 69 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8075 (p) REVERT: H 71 THR cc_start: 0.8160 (t) cc_final: 0.7933 (p) REVERT: H 90 ASP cc_start: 0.8061 (m-30) cc_final: 0.7815 (t0) REVERT: H 114 GLN cc_start: 0.8116 (pm20) cc_final: 0.7731 (pm20) REVERT: H 145 LEU cc_start: 0.8303 (mt) cc_final: 0.7949 (mt) REVERT: H 187 SER cc_start: 0.7959 (t) cc_final: 0.7609 (m) REVERT: H 216 LYS cc_start: 0.8622 (tppt) cc_final: 0.8362 (tppp) REVERT: H 217 LYS cc_start: 0.8412 (tttt) cc_final: 0.8137 (tttt) REVERT: L 22 SER cc_start: 0.8210 (p) cc_final: 0.7919 (m) REVERT: L 89 GLN cc_start: 0.7988 (tt0) cc_final: 0.7686 (tt0) REVERT: L 164 SER cc_start: 0.8567 (t) cc_final: 0.8017 (p) REVERT: L 173 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8362 (p) REVERT: L 175 TYR cc_start: 0.8207 (m-80) cc_final: 0.7797 (m-80) REVERT: L 201 GLN cc_start: 0.8070 (tt0) cc_final: 0.7800 (tt0) outliers start: 29 outliers final: 25 residues processed: 171 average time/residue: 0.1403 time to fit residues: 32.0429 Evaluate side-chains 180 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 160 ASN Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.0030 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 29 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 4965 Z= 0.221 Angle : 0.675 12.504 6766 Z= 0.335 Chirality : 0.046 0.262 750 Planarity : 0.005 0.037 867 Dihedral : 6.665 53.274 698 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 5.36 % Allowed : 24.58 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.32 (0.34), residues: 619 helix: -4.27 (1.12), residues: 12 sheet: -0.79 (0.36), residues: 220 loop : -1.99 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 47 HIS 0.002 0.001 HIS L 90 PHE 0.037 0.003 PHE A 416 TYR 0.033 0.002 TYR A 442 ARG 0.003 0.000 ARG L 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1238 Ramachandran restraints generated. 619 Oldfield, 0 Emsley, 619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 334 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.6990 (m-10) REVERT: A 436 TYR cc_start: 0.7977 (m-80) cc_final: 0.7706 (m-80) REVERT: A 447 LYS cc_start: 0.8017 (mttm) cc_final: 0.7688 (mttm) REVERT: A 457 ASN cc_start: 0.8123 (t0) cc_final: 0.7725 (t0) REVERT: H 36 TRP cc_start: 0.7656 (m100) cc_final: 0.7418 (m100) REVERT: H 69 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8074 (p) REVERT: H 90 ASP cc_start: 0.8063 (m-30) cc_final: 0.7797 (t0) REVERT: H 91 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7940 (p) REVERT: H 114 GLN cc_start: 0.8096 (pm20) cc_final: 0.7728 (pm20) REVERT: H 145 LEU cc_start: 0.8315 (mt) cc_final: 0.7969 (mt) REVERT: H 187 SER cc_start: 0.7915 (t) cc_final: 0.7583 (m) REVERT: H 216 LYS cc_start: 0.8605 (tppt) cc_final: 0.8330 (tppp) REVERT: H 217 LYS cc_start: 0.8395 (tttt) cc_final: 0.8120 (tttt) REVERT: L 22 SER cc_start: 0.8210 (p) cc_final: 0.7913 (m) REVERT: L 89 GLN cc_start: 0.7985 (tt0) cc_final: 0.7687 (tt0) REVERT: L 164 SER cc_start: 0.8563 (t) cc_final: 0.7998 (p) REVERT: L 173 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8371 (p) REVERT: L 201 GLN cc_start: 0.8063 (tt0) cc_final: 0.7793 (tt0) outliers start: 29 outliers final: 23 residues processed: 170 average time/residue: 0.1311 time to fit residues: 29.8800 Evaluate side-chains 178 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 CYS Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 338 TYR Chi-restraints excluded: chain A residue 356 TYR Chi-restraints excluded: chain A residue 408 TYR Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 TYR Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 47 TRP Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 110 ARG Chi-restraints excluded: chain L residue 111 THR Chi-restraints excluded: chain L residue 152 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 171 LYS Chi-restraints excluded: chain L residue 173 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 55 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.141657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.125912 restraints weight = 7373.260| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.81 r_work: 0.3664 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4965 Z= 0.207 Angle : 0.665 12.379 6766 Z= 0.329 Chirality : 0.046 0.255 750 Planarity : 0.005 0.040 867 Dihedral : 6.645 53.688 698 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 4.81 % Allowed : 24.58 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.25 (0.35), residues: 619 helix: -4.17 (1.21), residues: 12 sheet: -0.76 (0.36), residues: 220 loop : -1.93 (0.33), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 47 HIS 0.003 0.001 HIS L 90 PHE 0.035 0.003 PHE A 416 TYR 0.032 0.001 TYR A 442 ARG 0.003 0.000 ARG L 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1709.86 seconds wall clock time: 31 minutes 34.14 seconds (1894.14 seconds total)