Starting phenix.real_space_refine on Mon Mar 11 00:30:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/03_2024/8bv5_16255_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/03_2024/8bv5_16255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/03_2024/8bv5_16255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/03_2024/8bv5_16255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/03_2024/8bv5_16255_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bv5_16255/03_2024/8bv5_16255_updated.pdb" } resolution = 3.54 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= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 3971 2.51 5 N 1107 2.21 5 O 1179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 454": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A TYR 1042": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6296 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3518 Classifications: {'peptide': 437} Link IDs: {'PTRANS': 9, 'TRANS': 427} Chain breaks: 4 Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2716 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 11, 'TRANS': 318} Chain breaks: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'FOK': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.08, per 1000 atoms: 0.65 Number of scatterers: 6296 At special positions: 0 Unit cell: (112.2, 97.02, 82.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 35 16.00 P 3 15.00 Mg 1 11.99 O 1179 8.00 N 1107 7.00 C 3971 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 457 " - pdb=" SG CYS A 469 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 7 sheets defined 44.9% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 382 through 392 removed outlier: 4.209A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 428 No H-bonds generated for 'chain 'A' and resid 425 through 428' Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.549A pdb=" N HIS A 455 " --> pdb=" O LEU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 534 through 545 Processing helix chain 'A' and resid 555 through 561 removed outlier: 3.951A pdb=" N CYS A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 956 Processing helix chain 'A' and resid 959 through 966 Processing helix chain 'A' and resid 991 through 996 removed outlier: 3.753A pdb=" N ALA A 994 " --> pdb=" O PRO A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1024 Processing helix chain 'A' and resid 1060 through 1082 Processing helix chain 'A' and resid 1115 through 1125 Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 89 through 112 removed outlier: 3.907A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 3.713A pdb=" N PHE B 126 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 157 through 164 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 173 through 180 removed outlier: 4.162A pdb=" N GLN B 176 " --> pdb=" O ASP B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 No H-bonds generated for 'chain 'B' and resid 182 through 185' Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 228 through 237 removed outlier: 4.259A pdb=" N ARG B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP B 234 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE B 235 " --> pdb=" O ARG B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 265 through 277 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 332 through 351 Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.941A pdb=" N LEU B 388 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 410 through 412 Processing sheet with id= B, first strand: chain 'A' and resid 415 through 417 Processing sheet with id= C, first strand: chain 'A' and resid 976 through 980 removed outlier: 3.925A pdb=" N TYR A 976 " --> pdb=" O VAL A1102 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1090 through 1096 removed outlier: 3.683A pdb=" N LYS A1036 " --> pdb=" O MET A1043 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL A1045 " --> pdb=" O LYS A1034 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N LYS A1034 " --> pdb=" O VAL A1045 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 457 through 463 removed outlier: 4.186A pdb=" N LEU A 458 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL A 470 " --> pdb=" O LEU A 458 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR A 468 " --> pdb=" O ILE A 460 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ILE A 462 " --> pdb=" O CYS A 466 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS A 466 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 40 through 45 removed outlier: 7.051A pdb=" N ASN B 218 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LEU B 43 " --> pdb=" O ASN B 218 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N HIS B 220 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU B 45 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N PHE B 222 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.250A pdb=" N ILE B 288 " --> pdb=" O PHE B 246 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL B 248 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE B 290 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR B 360 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU B 291 " --> pdb=" O TYR B 360 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N HIS B 362 " --> pdb=" O LEU B 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 267 hydrogen bonds defined for protein. 714 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: 1.74 Time building geometry restraints manager: 2.64 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: 1069 1.32 - 1.44: 1723 1.44 - 1.57: 3570 1.57 - 1.69: 5 1.69 - 1.82: 53 Bond restraints: 6420 Sorted by residual: bond pdb=" C8 FOK A1301 " pdb=" O1 FOK A1301 " ideal model delta sigma weight residual 1.419 1.450 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" CB VAL A 376 " pdb=" CG2 VAL A 376 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.30e+00 bond pdb=" CG LEU A 953 " pdb=" CD2 LEU A 953 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.66e+00 bond pdb=" C12 FOK A1301 " pdb=" C13 FOK A1301 " ideal model delta sigma weight residual 1.550 1.525 0.025 2.00e-02 2.50e+03 1.62e+00 bond pdb=" C7 FOK A1301 " pdb=" O4 FOK A1301 " ideal model delta sigma weight residual 1.430 1.455 -0.025 2.00e-02 2.50e+03 1.58e+00 ... (remaining 6415 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.79: 85 105.79 - 112.89: 3449 112.89 - 120.00: 2276 120.00 - 127.10: 2803 127.10 - 134.21: 65 Bond angle restraints: 8678 Sorted by residual: angle pdb=" CB MET B 221 " pdb=" CG MET B 221 " pdb=" SD MET B 221 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.07e+00 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 127.25 -5.71 1.91e+00 2.74e-01 8.94e+00 angle pdb=" CA MET B 110 " pdb=" CB MET B 110 " pdb=" CG MET B 110 " ideal model delta sigma weight residual 114.10 119.49 -5.39 2.00e+00 2.50e-01 7.26e+00 angle pdb=" CB MET B 110 " pdb=" CG MET B 110 " pdb=" SD MET B 110 " ideal model delta sigma weight residual 112.70 120.72 -8.02 3.00e+00 1.11e-01 7.15e+00 angle pdb=" CA MET A 491 " pdb=" CB MET A 491 " pdb=" CG MET A 491 " ideal model delta sigma weight residual 114.10 118.88 -4.78 2.00e+00 2.50e-01 5.70e+00 ... (remaining 8673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3212 17.98 - 35.96: 522 35.96 - 53.94: 139 53.94 - 71.92: 22 71.92 - 89.90: 20 Dihedral angle restraints: 3915 sinusoidal: 1681 harmonic: 2234 Sorted by residual: dihedral pdb=" CB CYS A 457 " pdb=" SG CYS A 457 " pdb=" SG CYS A 469 " pdb=" CB CYS A 469 " ideal model delta sinusoidal sigma weight residual -86.00 -132.37 46.37 1 1.00e+01 1.00e-02 2.98e+01 dihedral pdb=" CA ASN A1003 " pdb=" C ASN A1003 " pdb=" N ASN A1004 " pdb=" CA ASN A1004 " ideal model delta harmonic sigma weight residual 180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA HIS A 552 " pdb=" C HIS A 552 " pdb=" N ILE A 553 " pdb=" CA ILE A 553 " ideal model delta harmonic sigma weight residual -180.00 -162.60 -17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 749 0.051 - 0.102: 162 0.102 - 0.152: 27 0.152 - 0.203: 6 0.203 - 0.254: 2 Chirality restraints: 946 Sorted by residual: chirality pdb=" C8 FOK A1301 " pdb=" C7 FOK A1301 " pdb=" C9 FOK A1301 " pdb=" O1 FOK A1301 " both_signs ideal model delta sigma weight residual False 2.90 2.65 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR A 494 " pdb=" CA THR A 494 " pdb=" OG1 THR A 494 " pdb=" CG2 THR A 494 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C13 FOK A1301 " pdb=" C12 FOK A1301 " pdb=" C16 FOK A1301 " pdb=" O1 FOK A1301 " both_signs ideal model delta sigma weight residual False -2.37 -2.56 0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 943 not shown) Planarity restraints: 1118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO B 115 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 995 " -0.006 2.00e-02 2.50e+03 1.26e-02 1.59e+00 pdb=" CG ASP A 995 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP A 995 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 995 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 239 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C ASN B 239 " -0.019 2.00e-02 2.50e+03 pdb=" O ASN B 239 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP B 240 " 0.006 2.00e-02 2.50e+03 ... (remaining 1115 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 56 2.53 - 3.12: 4968 3.12 - 3.71: 10425 3.71 - 4.31: 13424 4.31 - 4.90: 21815 Nonbonded interactions: 50688 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 1.934 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 1.960 2.170 nonbonded pdb=" OG1 THR B 204 " pdb="MG MG B 502 " model vdw 2.119 2.170 nonbonded pdb=" OG1 THR A1000 " pdb=" OD1 ASN A1003 " model vdw 2.179 2.440 nonbonded pdb=" OG1 THR B 204 " pdb=" O2G GSP B 501 " model vdw 2.184 2.440 ... (remaining 50683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 16.900 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.400 Find NCS groups from input model: 0.170 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 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 : 0.003 0.050 6420 Z= 0.228 Angle : 0.665 9.037 8678 Z= 0.333 Chirality : 0.046 0.254 946 Planarity : 0.003 0.033 1118 Dihedral : 19.374 89.899 2464 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.59 % Allowed : 35.19 % Favored : 64.22 % 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: -0.26 (0.31), residues: 751 helix: 0.94 (0.28), residues: 346 sheet: 0.19 (0.59), residues: 87 loop : -1.55 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.008 0.001 HIS A 582 PHE 0.016 0.001 PHE B 178 TYR 0.018 0.001 TYR A 468 ARG 0.008 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 454 GLU cc_start: 0.7148 (tp30) cc_final: 0.6748 (tm-30) REVERT: A 555 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7537 (tttt) REVERT: A 971 ASP cc_start: 0.6310 (m-30) cc_final: 0.5609 (t70) REVERT: B 64 HIS cc_start: 0.7098 (p-80) cc_final: 0.6652 (p90) REVERT: B 375 VAL cc_start: 0.4423 (t) cc_final: 0.4208 (m) outliers start: 4 outliers final: 1 residues processed: 114 average time/residue: 0.2038 time to fit residues: 30.2322 Evaluate side-chains 89 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 88 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 582 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 0.0070 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1109 GLN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6420 Z= 0.200 Angle : 0.580 5.662 8678 Z= 0.299 Chirality : 0.043 0.270 946 Planarity : 0.004 0.044 1118 Dihedral : 6.130 49.618 933 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 4.69 % Allowed : 32.84 % Favored : 62.46 % 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: -0.26 (0.31), residues: 751 helix: 0.98 (0.28), residues: 336 sheet: 0.56 (0.62), residues: 77 loop : -1.58 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 281 HIS 0.006 0.001 HIS B 387 PHE 0.022 0.002 PHE B 340 TYR 0.021 0.001 TYR A 468 ARG 0.003 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 91 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 419 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.6667 (t80) REVERT: A 448 PHE cc_start: 0.4661 (OUTLIER) cc_final: 0.4275 (t80) REVERT: A 454 GLU cc_start: 0.7275 (tp30) cc_final: 0.6876 (tm-30) REVERT: A 555 LYS cc_start: 0.8056 (ttpt) cc_final: 0.7560 (tttt) REVERT: A 971 ASP cc_start: 0.6449 (m-30) cc_final: 0.5755 (t0) REVERT: A 1143 LYS cc_start: 0.5208 (OUTLIER) cc_final: 0.4969 (mmtm) REVERT: B 64 HIS cc_start: 0.6997 (p-80) cc_final: 0.6491 (p90) REVERT: B 375 VAL cc_start: 0.4565 (t) cc_final: 0.4298 (m) outliers start: 32 outliers final: 13 residues processed: 113 average time/residue: 0.1658 time to fit residues: 25.9338 Evaluate side-chains 96 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 80 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1143 LYS Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 GLN A 480 HIS A 528 GLN A1133 GLN ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6420 Z= 0.271 Angle : 0.627 7.852 8678 Z= 0.323 Chirality : 0.045 0.184 946 Planarity : 0.004 0.033 1118 Dihedral : 5.503 27.379 931 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.92 % Favored : 92.94 % Rotamer: Outliers : 6.01 % Allowed : 31.67 % Favored : 62.32 % 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: -0.55 (0.30), residues: 751 helix: 0.75 (0.28), residues: 339 sheet: 0.58 (0.61), residues: 78 loop : -1.82 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 281 HIS 0.008 0.001 HIS A 948 PHE 0.042 0.002 PHE B 142 TYR 0.022 0.002 TYR A 468 ARG 0.003 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 86 time to evaluate : 0.766 Fit side-chains REVERT: A 405 HIS cc_start: 0.8124 (OUTLIER) cc_final: 0.7612 (t70) REVERT: A 419 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6775 (t80) REVERT: A 454 GLU cc_start: 0.7392 (tp30) cc_final: 0.6963 (tm-30) REVERT: A 486 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6366 (mm-30) REVERT: A 541 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6867 (mmmt) REVERT: A 555 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7699 (tttt) REVERT: A 971 ASP cc_start: 0.6869 (OUTLIER) cc_final: 0.6049 (t0) REVERT: A 1029 PHE cc_start: 0.5759 (OUTLIER) cc_final: 0.5344 (m-80) REVERT: A 1151 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.4633 (p90) REVERT: B 56 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6498 (tt) REVERT: B 64 HIS cc_start: 0.7105 (p-80) cc_final: 0.6551 (p90) outliers start: 41 outliers final: 20 residues processed: 113 average time/residue: 0.1685 time to fit residues: 26.2334 Evaluate side-chains 104 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 76 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 541 LYS Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 971 ASP Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.0470 chunk 19 optimal weight: 5.9990 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 427 ASN A 528 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6420 Z= 0.199 Angle : 0.580 8.232 8678 Z= 0.296 Chirality : 0.044 0.283 946 Planarity : 0.004 0.047 1118 Dihedral : 5.132 27.310 931 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 5.13 % Allowed : 33.28 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.30), residues: 751 helix: 0.81 (0.28), residues: 342 sheet: 0.59 (0.62), residues: 78 loop : -1.93 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 281 HIS 0.004 0.001 HIS A 948 PHE 0.017 0.002 PHE A 448 TYR 0.021 0.001 TYR A 468 ARG 0.002 0.000 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 85 time to evaluate : 0.726 Fit side-chains REVERT: A 405 HIS cc_start: 0.8121 (OUTLIER) cc_final: 0.7632 (t70) REVERT: A 419 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6787 (t80) REVERT: A 448 PHE cc_start: 0.4616 (OUTLIER) cc_final: 0.3994 (t80) REVERT: A 454 GLU cc_start: 0.7448 (tp30) cc_final: 0.6869 (tm-30) REVERT: A 455 HIS cc_start: 0.5595 (OUTLIER) cc_final: 0.4545 (m90) REVERT: A 486 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5862 (mm-30) REVERT: A 555 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7710 (tttt) REVERT: A 971 ASP cc_start: 0.6831 (m-30) cc_final: 0.6013 (t0) REVERT: A 1029 PHE cc_start: 0.5817 (OUTLIER) cc_final: 0.5456 (m-80) REVERT: B 56 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6554 (tt) REVERT: B 64 HIS cc_start: 0.7032 (p-80) cc_final: 0.6370 (p90) outliers start: 35 outliers final: 21 residues processed: 111 average time/residue: 0.1748 time to fit residues: 26.3411 Evaluate side-chains 108 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 80 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 62 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 0.0470 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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: 0.6470 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6420 Z= 0.176 Angle : 0.560 9.938 8678 Z= 0.284 Chirality : 0.044 0.319 946 Planarity : 0.003 0.043 1118 Dihedral : 4.903 27.899 931 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.26 % Favored : 93.61 % Rotamer: Outliers : 6.30 % Allowed : 32.55 % Favored : 61.14 % 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: -0.37 (0.30), residues: 751 helix: 0.96 (0.28), residues: 342 sheet: 0.77 (0.63), residues: 78 loop : -1.87 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 281 HIS 0.003 0.001 HIS A 948 PHE 0.015 0.001 PHE A 448 TYR 0.021 0.001 TYR A 468 ARG 0.002 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 85 time to evaluate : 0.707 Fit side-chains REVERT: A 405 HIS cc_start: 0.8069 (OUTLIER) cc_final: 0.7588 (t70) REVERT: A 419 PHE cc_start: 0.7486 (OUTLIER) cc_final: 0.6765 (t80) REVERT: A 448 PHE cc_start: 0.4834 (OUTLIER) cc_final: 0.4435 (t80) REVERT: A 454 GLU cc_start: 0.7502 (tp30) cc_final: 0.6943 (tm-30) REVERT: A 455 HIS cc_start: 0.5496 (OUTLIER) cc_final: 0.4579 (m90) REVERT: A 486 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.5921 (mm-30) REVERT: A 555 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7704 (tttt) REVERT: A 971 ASP cc_start: 0.6844 (OUTLIER) cc_final: 0.5972 (t0) REVERT: A 1151 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.4672 (p90) REVERT: B 56 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6484 (tt) REVERT: B 64 HIS cc_start: 0.6789 (p-80) cc_final: 0.6217 (p90) REVERT: B 119 LEU cc_start: 0.4490 (OUTLIER) cc_final: 0.3827 (mp) REVERT: B 385 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.8270 (tmm-80) REVERT: B 390 GLN cc_start: 0.3873 (OUTLIER) cc_final: 0.2546 (tm-30) outliers start: 43 outliers final: 22 residues processed: 117 average time/residue: 0.2010 time to fit residues: 30.7143 Evaluate side-chains 110 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 77 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 971 ASP Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 390 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 70 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6420 Z= 0.192 Angle : 0.580 11.299 8678 Z= 0.291 Chirality : 0.044 0.314 946 Planarity : 0.003 0.038 1118 Dihedral : 4.955 28.223 931 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 6.16 % Allowed : 32.11 % Favored : 61.73 % 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: -0.34 (0.30), residues: 751 helix: 0.97 (0.28), residues: 343 sheet: 0.74 (0.62), residues: 78 loop : -1.81 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 281 HIS 0.003 0.001 HIS A1082 PHE 0.053 0.002 PHE B 142 TYR 0.020 0.001 TYR A 468 ARG 0.004 0.000 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 85 time to evaluate : 0.756 Fit side-chains REVERT: A 405 HIS cc_start: 0.8106 (OUTLIER) cc_final: 0.7575 (t70) REVERT: A 419 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.6767 (t80) REVERT: A 448 PHE cc_start: 0.4840 (OUTLIER) cc_final: 0.4401 (t80) REVERT: A 454 GLU cc_start: 0.7578 (tp30) cc_final: 0.7008 (tm-30) REVERT: A 455 HIS cc_start: 0.5524 (OUTLIER) cc_final: 0.4607 (m90) REVERT: A 486 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6032 (mm-30) REVERT: A 555 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7779 (tttt) REVERT: A 971 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6014 (t0) REVERT: A 1029 PHE cc_start: 0.5805 (OUTLIER) cc_final: 0.5502 (m-80) REVERT: A 1151 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.4746 (p90) REVERT: B 56 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6534 (tt) REVERT: B 64 HIS cc_start: 0.6864 (p-80) cc_final: 0.6278 (p90) REVERT: B 119 LEU cc_start: 0.4486 (OUTLIER) cc_final: 0.3824 (mp) REVERT: B 385 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8297 (tmm-80) REVERT: B 390 GLN cc_start: 0.3836 (OUTLIER) cc_final: 0.2380 (tm-30) outliers start: 42 outliers final: 26 residues processed: 114 average time/residue: 0.1946 time to fit residues: 29.3303 Evaluate side-chains 118 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 80 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 465 ASP Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 550 ARG Chi-restraints excluded: chain A residue 971 ASP Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 390 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6420 Z= 0.236 Angle : 0.629 12.110 8678 Z= 0.315 Chirality : 0.045 0.319 946 Planarity : 0.004 0.039 1118 Dihedral : 5.159 28.954 931 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.06 % Favored : 92.81 % Rotamer: Outliers : 6.16 % Allowed : 32.26 % Favored : 61.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.30), residues: 751 helix: 0.89 (0.28), residues: 343 sheet: 0.67 (0.62), residues: 78 loop : -1.83 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 281 HIS 0.005 0.001 HIS A1082 PHE 0.020 0.002 PHE A 448 TYR 0.020 0.001 TYR A 468 ARG 0.004 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 80 time to evaluate : 0.725 Fit side-chains REVERT: A 405 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7552 (t70) REVERT: A 419 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.6836 (t80) REVERT: A 448 PHE cc_start: 0.4733 (OUTLIER) cc_final: 0.4278 (t80) REVERT: A 454 GLU cc_start: 0.7585 (tp30) cc_final: 0.7038 (tm-30) REVERT: A 455 HIS cc_start: 0.5491 (OUTLIER) cc_final: 0.4632 (m90) REVERT: A 486 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6033 (mm-30) REVERT: A 555 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7807 (tttt) REVERT: A 971 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6067 (t0) REVERT: A 1029 PHE cc_start: 0.5819 (OUTLIER) cc_final: 0.5526 (m-80) REVERT: A 1144 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.6015 (m-30) REVERT: A 1151 TYR cc_start: 0.6860 (OUTLIER) cc_final: 0.4755 (p90) REVERT: B 56 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6488 (tt) REVERT: B 64 HIS cc_start: 0.6954 (p-80) cc_final: 0.6346 (p90) REVERT: B 119 LEU cc_start: 0.4492 (OUTLIER) cc_final: 0.3841 (mp) REVERT: B 385 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8356 (tmm-80) REVERT: B 390 GLN cc_start: 0.4025 (OUTLIER) cc_final: 0.2474 (tm-30) outliers start: 42 outliers final: 24 residues processed: 110 average time/residue: 0.1831 time to fit residues: 27.1732 Evaluate side-chains 115 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 78 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 971 ASP Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 385 ARG Chi-restraints excluded: chain B residue 390 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6420 Z= 0.206 Angle : 0.610 12.537 8678 Z= 0.304 Chirality : 0.044 0.341 946 Planarity : 0.004 0.038 1118 Dihedral : 5.060 29.104 931 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.52 % Favored : 93.34 % Rotamer: Outliers : 6.60 % Allowed : 32.11 % Favored : 61.29 % 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: -0.39 (0.30), residues: 751 helix: 0.95 (0.28), residues: 340 sheet: 0.69 (0.61), residues: 78 loop : -1.84 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 281 HIS 0.004 0.001 HIS A1082 PHE 0.055 0.002 PHE B 142 TYR 0.021 0.001 TYR A 468 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 83 time to evaluate : 0.799 Fit side-chains REVERT: A 405 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7556 (t70) REVERT: A 419 PHE cc_start: 0.7527 (OUTLIER) cc_final: 0.6848 (t80) REVERT: A 448 PHE cc_start: 0.4860 (OUTLIER) cc_final: 0.4466 (t80) REVERT: A 454 GLU cc_start: 0.7571 (tp30) cc_final: 0.7010 (tm-30) REVERT: A 455 HIS cc_start: 0.5505 (OUTLIER) cc_final: 0.4650 (m90) REVERT: A 486 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6051 (mm-30) REVERT: A 555 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7827 (tttt) REVERT: A 971 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6057 (t0) REVERT: A 1029 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5534 (m-80) REVERT: A 1144 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.5989 (m-30) REVERT: A 1150 ASP cc_start: 0.5635 (OUTLIER) cc_final: 0.5404 (m-30) REVERT: A 1151 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.4770 (p90) REVERT: B 37 TYR cc_start: 0.4913 (m-80) cc_final: 0.4651 (m-80) REVERT: B 56 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6564 (tt) REVERT: B 64 HIS cc_start: 0.6968 (p-80) cc_final: 0.6353 (p90) REVERT: B 119 LEU cc_start: 0.4525 (OUTLIER) cc_final: 0.3892 (mp) REVERT: B 390 GLN cc_start: 0.4089 (OUTLIER) cc_final: 0.2540 (tm-30) outliers start: 45 outliers final: 26 residues processed: 116 average time/residue: 0.1863 time to fit residues: 28.6681 Evaluate side-chains 116 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 77 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 971 ASP Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 357 HIS Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 390 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6420 Z= 0.212 Angle : 0.639 13.016 8678 Z= 0.314 Chirality : 0.045 0.359 946 Planarity : 0.004 0.041 1118 Dihedral : 5.098 29.770 931 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.92 % Favored : 92.94 % Rotamer: Outliers : 6.16 % Allowed : 32.40 % Favored : 61.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.30), residues: 751 helix: 1.04 (0.28), residues: 334 sheet: 0.66 (0.61), residues: 78 loop : -1.80 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 277 HIS 0.004 0.001 HIS A1082 PHE 0.017 0.002 PHE A1147 TYR 0.020 0.001 TYR A 468 ARG 0.002 0.000 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 83 time to evaluate : 0.937 Fit side-chains REVERT: A 419 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6894 (t80) REVERT: A 448 PHE cc_start: 0.4880 (OUTLIER) cc_final: 0.4537 (t80) REVERT: A 454 GLU cc_start: 0.7563 (tp30) cc_final: 0.7001 (tm-30) REVERT: A 455 HIS cc_start: 0.5460 (OUTLIER) cc_final: 0.4626 (m90) REVERT: A 486 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.6045 (mm-30) REVERT: A 555 LYS cc_start: 0.8270 (ttpt) cc_final: 0.7845 (tttt) REVERT: A 971 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6072 (t0) REVERT: A 1029 PHE cc_start: 0.5789 (OUTLIER) cc_final: 0.5471 (m-80) REVERT: A 1144 ASP cc_start: 0.6591 (OUTLIER) cc_final: 0.5998 (m-30) REVERT: A 1150 ASP cc_start: 0.5652 (OUTLIER) cc_final: 0.5397 (m-30) REVERT: A 1151 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.4878 (p90) REVERT: B 37 TYR cc_start: 0.4919 (m-80) cc_final: 0.4699 (m-80) REVERT: B 56 ILE cc_start: 0.6902 (OUTLIER) cc_final: 0.6539 (tt) REVERT: B 64 HIS cc_start: 0.6998 (p-80) cc_final: 0.6346 (p90) REVERT: B 119 LEU cc_start: 0.4495 (OUTLIER) cc_final: 0.3818 (mp) outliers start: 42 outliers final: 25 residues processed: 114 average time/residue: 0.1767 time to fit residues: 27.4848 Evaluate side-chains 116 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 80 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 971 ASP Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 8.9990 chunk 60 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6420 Z= 0.223 Angle : 0.647 13.238 8678 Z= 0.318 Chirality : 0.045 0.365 946 Planarity : 0.004 0.040 1118 Dihedral : 5.173 30.577 931 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.99 % Favored : 93.87 % Rotamer: Outliers : 5.72 % Allowed : 33.43 % Favored : 60.85 % 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: -0.40 (0.30), residues: 751 helix: 0.91 (0.28), residues: 340 sheet: 0.66 (0.60), residues: 79 loop : -1.81 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 277 HIS 0.004 0.001 HIS A1082 PHE 0.044 0.002 PHE B 142 TYR 0.022 0.001 TYR A 468 ARG 0.003 0.000 ARG B 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 86 time to evaluate : 0.720 Fit side-chains REVERT: A 405 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7486 (t70) REVERT: A 419 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.6859 (t80) REVERT: A 448 PHE cc_start: 0.4854 (OUTLIER) cc_final: 0.4521 (t80) REVERT: A 454 GLU cc_start: 0.7587 (tp30) cc_final: 0.6997 (tm-30) REVERT: A 455 HIS cc_start: 0.5382 (OUTLIER) cc_final: 0.4718 (m90) REVERT: A 486 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5921 (mm-30) REVERT: A 555 LYS cc_start: 0.8283 (ttpt) cc_final: 0.7875 (tttt) REVERT: A 971 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6046 (t0) REVERT: A 1029 PHE cc_start: 0.5803 (OUTLIER) cc_final: 0.5520 (m-80) REVERT: A 1144 ASP cc_start: 0.6553 (OUTLIER) cc_final: 0.5987 (m-30) REVERT: A 1150 ASP cc_start: 0.5661 (OUTLIER) cc_final: 0.5370 (m-30) REVERT: A 1151 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.4950 (p90) REVERT: B 37 TYR cc_start: 0.4776 (m-80) cc_final: 0.4555 (m-80) REVERT: B 56 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6510 (tt) REVERT: B 64 HIS cc_start: 0.7057 (p-80) cc_final: 0.6452 (p90) REVERT: B 119 LEU cc_start: 0.4374 (OUTLIER) cc_final: 0.3735 (mp) REVERT: B 290 PHE cc_start: 0.5448 (m-10) cc_final: 0.4872 (m-10) outliers start: 39 outliers final: 24 residues processed: 115 average time/residue: 0.1812 time to fit residues: 28.4356 Evaluate side-chains 121 residues out of total 682 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 85 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 419 PHE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 448 PHE Chi-restraints excluded: chain A residue 453 HIS Chi-restraints excluded: chain A residue 455 HIS Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 971 ASP Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1029 PHE Chi-restraints excluded: chain A residue 1038 ILE Chi-restraints excluded: chain A residue 1046 SER Chi-restraints excluded: chain A residue 1085 ASN Chi-restraints excluded: chain A residue 1103 ILE Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1144 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1151 TYR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 126 PHE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 201 ARG Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 264 ASN Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 372 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 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 = 0.4550 r_free = 0.4550 target = 0.192587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.164471 restraints weight = 10322.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.168839 restraints weight = 5483.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.171711 restraints weight = 3563.106| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6420 Z= 0.202 Angle : 0.642 13.813 8678 Z= 0.315 Chirality : 0.044 0.349 946 Planarity : 0.004 0.042 1118 Dihedral : 5.091 29.990 931 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.13 % Favored : 93.74 % Rotamer: Outliers : 5.72 % Allowed : 33.28 % Favored : 61.00 % 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: -0.34 (0.30), residues: 751 helix: 0.96 (0.28), residues: 340 sheet: 0.77 (0.60), residues: 79 loop : -1.80 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 277 HIS 0.004 0.001 HIS A1082 PHE 0.017 0.002 PHE A1147 TYR 0.021 0.001 TYR A 468 ARG 0.003 0.000 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1784.88 seconds wall clock time: 33 minutes 37.43 seconds (2017.43 seconds total)