Starting phenix.real_space_refine on Thu Nov 14 14:26:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/11_2024/8i4h_35173.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/11_2024/8i4h_35173.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/11_2024/8i4h_35173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/11_2024/8i4h_35173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/11_2024/8i4h_35173.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/11_2024/8i4h_35173.cif" } resolution = 3.81 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= 0.002 sd= 0.029 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 32 5.16 5 C 4194 2.51 5 N 1075 2.21 5 O 1238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6539 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4724 Classifications: {'peptide': 598} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 32, 'TRANS': 565} Chain breaks: 6 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1815 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 8, 'TRANS': 226} Chain breaks: 1 Time building chain proxies: 4.25, per 1000 atoms: 0.65 Number of scatterers: 6539 At special positions: 0 Unit cell: (71.288, 90.44, 131.936, 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 32 16.00 O 1238 8.00 N 1075 7.00 C 4194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 234 " 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: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 19 sheets defined 3.5% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 406 through 411 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.687A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 4.348A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 removed outlier: 3.700A pdb=" N THR B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.724A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.923A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.688A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 95 removed outlier: 5.911A pdb=" N SER A 203 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.611A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.528A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 651 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N THR A 645 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.883A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL A 512 " --> pdb=" O ASP A 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.371A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 655 through 660 removed outlier: 6.527A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.862A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 674 through 675 Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.662A pdb=" N MET B 82 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.800A pdb=" N ARG B 56 " --> pdb=" O TYR B 52 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET B 34 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 37 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 94 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR B 93 " --> pdb=" O THR B 112 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 112 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 149 through 150 Processing sheet with id=AB9, first strand: chain 'B' and resid 157 through 161 removed outlier: 3.529A pdb=" N THR B 207 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173 removed outlier: 3.631A pdb=" N ALA B 235 " --> pdb=" O SER B 173 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 264 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: 1.96 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2080 1.35 - 1.46: 1704 1.46 - 1.58: 2878 1.58 - 1.70: 0 1.70 - 1.81: 41 Bond restraints: 6703 Sorted by residual: bond pdb=" C GLU A 212 " pdb=" N PRO A 213 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.92e-01 bond pdb=" C ILE A 664 " pdb=" O ILE A 664 " ideal model delta sigma weight residual 1.240 1.231 0.009 1.26e-02 6.30e+03 5.02e-01 bond pdb=" C GLN A 173 " pdb=" N PRO A 174 " ideal model delta sigma weight residual 1.330 1.338 -0.008 1.19e-02 7.06e+03 4.31e-01 bond pdb=" CB PRO A 330 " pdb=" CG PRO A 330 " ideal model delta sigma weight residual 1.492 1.523 -0.031 5.00e-02 4.00e+02 3.96e-01 bond pdb=" N ASP B 26 " pdb=" CA ASP B 26 " ideal model delta sigma weight residual 1.460 1.469 -0.009 1.54e-02 4.22e+03 3.31e-01 ... (remaining 6698 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 8836 1.03 - 2.06: 207 2.06 - 3.09: 64 3.09 - 4.12: 9 4.12 - 5.15: 2 Bond angle restraints: 9118 Sorted by residual: angle pdb=" N ASP A 80 " pdb=" CA ASP A 80 " pdb=" C ASP A 80 " ideal model delta sigma weight residual 114.56 111.04 3.52 1.27e+00 6.20e-01 7.68e+00 angle pdb=" CA ASP A 80 " pdb=" C ASP A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 119.26 116.87 2.39 1.14e+00 7.69e-01 4.40e+00 angle pdb=" CA ASP A 80 " pdb=" C ASP A 80 " pdb=" O ASP A 80 " ideal model delta sigma weight residual 118.55 120.50 -1.95 1.14e+00 7.69e-01 2.94e+00 angle pdb=" C SER B 25 " pdb=" N ASP B 26 " pdb=" CA ASP B 26 " ideal model delta sigma weight residual 122.46 124.71 -2.25 1.41e+00 5.03e-01 2.55e+00 angle pdb=" C PHE A 559 " pdb=" N LEU A 560 " pdb=" CA LEU A 560 " ideal model delta sigma weight residual 121.80 125.69 -3.89 2.44e+00 1.68e-01 2.54e+00 ... (remaining 9113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 3736 16.03 - 32.05: 166 32.05 - 48.08: 35 48.08 - 64.10: 6 64.10 - 80.13: 1 Dihedral angle restraints: 3944 sinusoidal: 1525 harmonic: 2419 Sorted by residual: dihedral pdb=" N LYS A 424 " pdb=" CA LYS A 424 " pdb=" CB LYS A 424 " pdb=" CG LYS A 424 " ideal model delta sinusoidal sigma weight residual -180.00 -120.01 -59.99 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LEU A 390 " pdb=" CA LEU A 390 " pdb=" CB LEU A 390 " pdb=" CG LEU A 390 " ideal model delta sinusoidal sigma weight residual -60.00 -116.77 56.77 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" N PHE A 329 " pdb=" CA PHE A 329 " pdb=" CB PHE A 329 " pdb=" CG PHE A 329 " ideal model delta sinusoidal sigma weight residual -180.00 -125.13 -54.87 3 1.50e+01 4.44e-03 9.31e+00 ... (remaining 3941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 572 0.025 - 0.050: 259 0.050 - 0.076: 83 0.076 - 0.101: 60 0.101 - 0.126: 29 Chirality restraints: 1003 Sorted by residual: chirality pdb=" CA ILE A 101 " pdb=" N ILE A 101 " pdb=" C ILE A 101 " pdb=" CB ILE A 101 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA ILE A 584 " pdb=" N ILE A 584 " pdb=" C ILE A 584 " pdb=" CB ILE A 584 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA ILE A 235 " pdb=" N ILE A 235 " pdb=" C ILE A 235 " pdb=" CB ILE A 235 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1000 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 173 " 0.037 5.00e-02 4.00e+02 5.59e-02 5.00e+00 pdb=" N PRO A 174 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 321 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 322 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 336 " 0.019 5.00e-02 4.00e+02 2.83e-02 1.28e+00 pdb=" N PRO A 337 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 337 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 337 " 0.016 5.00e-02 4.00e+02 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1589 2.79 - 3.32: 5895 3.32 - 3.84: 10478 3.84 - 4.37: 11962 4.37 - 4.90: 20458 Nonbonded interactions: 50382 Sorted by model distance: nonbonded pdb=" O ASP B 89 " pdb=" OH TYR B 93 " model vdw 2.262 3.040 nonbonded pdb=" O VAL A 130 " pdb=" OG1 THR A 167 " model vdw 2.270 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.275 3.040 nonbonded pdb=" OG1 THR A 470 " pdb=" OG SER B 54 " model vdw 2.277 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.295 3.040 ... (remaining 50377 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 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.140 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 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 : 0.001 0.031 6703 Z= 0.095 Angle : 0.433 5.155 9118 Z= 0.240 Chirality : 0.040 0.126 1003 Planarity : 0.004 0.056 1175 Dihedral : 9.227 80.126 2367 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 5.85 % Allowed : 7.52 % Favored : 86.63 % 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: -4.65 (0.24), residues: 815 helix: -2.48 (1.17), residues: 14 sheet: -2.96 (0.34), residues: 172 loop : -3.44 (0.20), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 99 HIS 0.001 0.000 HIS A 49 PHE 0.005 0.001 PHE A 192 TYR 0.005 0.001 TYR B 169 ARG 0.001 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.5984 (t80) cc_final: 0.5726 (t80) REVERT: A 95 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7597 (tp) REVERT: A 177 MET cc_start: 0.6113 (mmt) cc_final: 0.5836 (mmt) REVERT: A 294 ASP cc_start: 0.7943 (p0) cc_final: 0.7654 (p0) REVERT: A 357 ARG cc_start: 0.6937 (ttp80) cc_final: 0.6561 (ttp80) REVERT: A 368 LEU cc_start: 0.7611 (mm) cc_final: 0.7289 (tp) REVERT: A 387 LEU cc_start: 0.8674 (mt) cc_final: 0.8255 (tp) REVERT: A 388 ASN cc_start: 0.7787 (m110) cc_final: 0.7455 (p0) REVERT: A 394 ASN cc_start: 0.7343 (m-40) cc_final: 0.7117 (m-40) REVERT: A 395 VAL cc_start: 0.7655 (m) cc_final: 0.7377 (t) REVERT: A 408 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7476 (ttp-170) REVERT: A 417 ASN cc_start: 0.7679 (t0) cc_final: 0.7403 (t0) REVERT: A 428 ASP cc_start: 0.7345 (p0) cc_final: 0.7010 (p0) REVERT: A 452 LEU cc_start: 0.7605 (mp) cc_final: 0.7186 (tt) REVERT: A 470 THR cc_start: 0.7394 (p) cc_final: 0.7114 (p) REVERT: A 490 PHE cc_start: 0.8416 (t80) cc_final: 0.8200 (t80) REVERT: A 537 LYS cc_start: 0.7724 (tppp) cc_final: 0.7195 (mmmm) REVERT: A 562 PHE cc_start: 0.6663 (t80) cc_final: 0.5858 (t80) REVERT: A 699 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8382 (pt) REVERT: B 82 MET cc_start: 0.8750 (mtt) cc_final: 0.8326 (mtt) REVERT: B 93 TYR cc_start: 0.6581 (m-80) cc_final: 0.5874 (m-80) REVERT: B 167 PHE cc_start: 0.6732 (m-80) cc_final: 0.6530 (m-80) REVERT: B 215 ASN cc_start: 0.8693 (m-40) cc_final: 0.8446 (t0) REVERT: B 252 THR cc_start: 0.8471 (t) cc_final: 0.8266 (p) outliers start: 42 outliers final: 14 residues processed: 270 average time/residue: 0.2225 time to fit residues: 76.0614 Evaluate side-chains 218 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 0.0870 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 87 ASN A 165 ASN A 173 GLN A 234 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 321 GLN A 360 ASN A 388 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN A 563 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 13 GLN B 81 GLN B 110 GLN B 141 GLN B 212 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6703 Z= 0.233 Angle : 0.636 7.475 9118 Z= 0.324 Chirality : 0.046 0.258 1003 Planarity : 0.005 0.054 1175 Dihedral : 6.645 81.968 950 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 6.55 % Allowed : 14.07 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.26), residues: 815 helix: -2.55 (1.20), residues: 16 sheet: -2.85 (0.35), residues: 177 loop : -2.91 (0.22), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 174 HIS 0.019 0.003 HIS A 519 PHE 0.034 0.001 PHE A 306 TYR 0.011 0.001 TYR A 160 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 231 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7415 (tp40) REVERT: A 67 VAL cc_start: 0.8232 (p) cc_final: 0.7543 (m) REVERT: A 92 PHE cc_start: 0.6541 (t80) cc_final: 0.6249 (t80) REVERT: A 177 MET cc_start: 0.6190 (mmt) cc_final: 0.5898 (mmt) REVERT: A 204 LYS cc_start: 0.8216 (tttp) cc_final: 0.7939 (tttp) REVERT: A 241 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8175 (mm) REVERT: A 265 TYR cc_start: 0.6695 (m-80) cc_final: 0.6394 (m-80) REVERT: A 357 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6715 (ttp80) REVERT: A 359 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7907 (t) REVERT: A 368 LEU cc_start: 0.8140 (mm) cc_final: 0.7570 (tp) REVERT: A 387 LEU cc_start: 0.8683 (mt) cc_final: 0.8346 (tp) REVERT: A 395 VAL cc_start: 0.7870 (m) cc_final: 0.7502 (m) REVERT: A 396 TYR cc_start: 0.7014 (m-80) cc_final: 0.6399 (m-10) REVERT: A 408 ARG cc_start: 0.8007 (ttp-170) cc_final: 0.7597 (ttp-170) REVERT: A 417 ASN cc_start: 0.7814 (t0) cc_final: 0.7438 (t0) REVERT: A 424 LYS cc_start: 0.8200 (tmtm) cc_final: 0.7864 (tmtm) REVERT: A 442 ASP cc_start: 0.8082 (p0) cc_final: 0.7784 (p0) REVERT: A 452 LEU cc_start: 0.7758 (mp) cc_final: 0.7243 (tt) REVERT: A 490 PHE cc_start: 0.8240 (t80) cc_final: 0.7988 (t80) REVERT: A 501 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7342 (t80) REVERT: A 528 LYS cc_start: 0.7697 (mttm) cc_final: 0.7160 (mttp) REVERT: A 537 LYS cc_start: 0.7927 (tppp) cc_final: 0.7498 (mmmm) REVERT: A 598 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8158 (tp) REVERT: B 38 ARG cc_start: 0.7249 (ttp-170) cc_final: 0.6663 (ttp-170) REVERT: B 64 LYS cc_start: 0.8263 (tptt) cc_final: 0.7940 (tptt) REVERT: B 93 TYR cc_start: 0.6802 (m-80) cc_final: 0.5866 (m-80) REVERT: B 97 SER cc_start: 0.7729 (OUTLIER) cc_final: 0.7403 (p) REVERT: B 189 ILE cc_start: 0.8709 (mm) cc_final: 0.8376 (mm) REVERT: B 252 THR cc_start: 0.8439 (t) cc_final: 0.8191 (m) outliers start: 47 outliers final: 24 residues processed: 256 average time/residue: 0.2454 time to fit residues: 79.1328 Evaluate side-chains 236 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6703 Z= 0.258 Angle : 0.672 8.589 9118 Z= 0.344 Chirality : 0.046 0.157 1003 Planarity : 0.005 0.058 1175 Dihedral : 6.806 80.862 940 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.80 % Favored : 89.20 % Rotamer: Outliers : 4.87 % Allowed : 19.22 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.27), residues: 815 helix: -1.96 (1.36), residues: 17 sheet: -2.58 (0.36), residues: 178 loop : -2.74 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP B 174 HIS 0.007 0.002 HIS A 519 PHE 0.042 0.002 PHE A 275 TYR 0.014 0.001 TYR B 107 ARG 0.004 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7849 (tm130) cc_final: 0.7461 (tp40) REVERT: A 67 VAL cc_start: 0.8563 (p) cc_final: 0.8042 (m) REVERT: A 86 PHE cc_start: 0.8536 (t80) cc_final: 0.8287 (t80) REVERT: A 177 MET cc_start: 0.6274 (mmt) cc_final: 0.5953 (mmt) REVERT: A 204 LYS cc_start: 0.8185 (tttp) cc_final: 0.7677 (tttp) REVERT: A 265 TYR cc_start: 0.6830 (m-80) cc_final: 0.6364 (m-80) REVERT: A 304 LYS cc_start: 0.8457 (mmtp) cc_final: 0.8232 (mmtp) REVERT: A 313 TYR cc_start: 0.6228 (m-80) cc_final: 0.5687 (m-80) REVERT: A 368 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8033 (tt) REVERT: A 387 LEU cc_start: 0.8669 (mt) cc_final: 0.8428 (mt) REVERT: A 391 CYS cc_start: 0.5063 (p) cc_final: 0.4339 (p) REVERT: A 396 TYR cc_start: 0.7005 (m-80) cc_final: 0.5927 (m-10) REVERT: A 401 VAL cc_start: 0.8116 (t) cc_final: 0.7710 (m) REVERT: A 408 ARG cc_start: 0.7976 (ttp-170) cc_final: 0.7596 (ttp-170) REVERT: A 417 ASN cc_start: 0.7925 (t0) cc_final: 0.7574 (t0) REVERT: A 424 LYS cc_start: 0.8301 (tmtm) cc_final: 0.7932 (tptp) REVERT: A 442 ASP cc_start: 0.8242 (p0) cc_final: 0.7881 (p0) REVERT: A 452 LEU cc_start: 0.7746 (mp) cc_final: 0.7195 (tt) REVERT: A 462 LYS cc_start: 0.8278 (tptp) cc_final: 0.8055 (tptp) REVERT: A 465 GLU cc_start: 0.6285 (mm-30) cc_final: 0.6031 (mm-30) REVERT: A 501 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7513 (t80) REVERT: A 537 LYS cc_start: 0.8056 (tppp) cc_final: 0.7456 (mmmm) REVERT: A 588 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8701 (p) REVERT: A 598 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8223 (tp) REVERT: B 64 LYS cc_start: 0.8235 (tptt) cc_final: 0.7947 (tptt) REVERT: B 93 TYR cc_start: 0.6688 (m-80) cc_final: 0.6132 (m-80) REVERT: B 96 VAL cc_start: 0.8900 (t) cc_final: 0.8619 (m) REVERT: B 107 TYR cc_start: 0.6161 (t80) cc_final: 0.5337 (t80) REVERT: B 158 LEU cc_start: 0.7900 (mm) cc_final: 0.7002 (mt) REVERT: B 159 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7989 (t) REVERT: B 189 ILE cc_start: 0.8733 (mm) cc_final: 0.8444 (mm) outliers start: 35 outliers final: 22 residues processed: 240 average time/residue: 0.2480 time to fit residues: 74.5002 Evaluate side-chains 227 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 200 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 231 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 38 optimal weight: 0.1980 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 540 ASN B 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6703 Z= 0.175 Angle : 0.635 7.803 9118 Z= 0.323 Chirality : 0.045 0.156 1003 Planarity : 0.005 0.064 1175 Dihedral : 6.678 81.307 938 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.78 % Favored : 88.22 % Rotamer: Outliers : 5.57 % Allowed : 19.22 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.27), residues: 815 helix: -1.91 (1.33), residues: 17 sheet: -2.49 (0.35), residues: 200 loop : -2.60 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 174 HIS 0.004 0.001 HIS A 519 PHE 0.035 0.002 PHE A 275 TYR 0.015 0.001 TYR B 107 ARG 0.008 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7642 (tm130) cc_final: 0.7225 (tp40) REVERT: A 67 VAL cc_start: 0.8350 (p) cc_final: 0.7880 (m) REVERT: A 86 PHE cc_start: 0.8518 (t80) cc_final: 0.8242 (t80) REVERT: A 177 MET cc_start: 0.6289 (mmt) cc_final: 0.5955 (mmt) REVERT: A 224 GLU cc_start: 0.7355 (pm20) cc_final: 0.6565 (pm20) REVERT: A 265 TYR cc_start: 0.6698 (m-80) cc_final: 0.6237 (m-80) REVERT: A 310 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8448 (mmmm) REVERT: A 313 TYR cc_start: 0.6101 (m-80) cc_final: 0.5573 (m-80) REVERT: A 359 SER cc_start: 0.8318 (m) cc_final: 0.7812 (t) REVERT: A 388 ASN cc_start: 0.8140 (p0) cc_final: 0.7585 (t0) REVERT: A 401 VAL cc_start: 0.7938 (OUTLIER) cc_final: 0.7477 (m) REVERT: A 408 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7529 (ttp-170) REVERT: A 417 ASN cc_start: 0.7819 (t0) cc_final: 0.7472 (t0) REVERT: A 424 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7630 (tptp) REVERT: A 442 ASP cc_start: 0.8328 (p0) cc_final: 0.7895 (p0) REVERT: A 452 LEU cc_start: 0.7490 (mp) cc_final: 0.7056 (tt) REVERT: A 490 PHE cc_start: 0.8077 (t80) cc_final: 0.7870 (t80) REVERT: A 501 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7511 (t80) REVERT: A 588 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8711 (p) REVERT: B 38 ARG cc_start: 0.7560 (ttp80) cc_final: 0.7327 (ttp80) REVERT: B 64 LYS cc_start: 0.8206 (tptt) cc_final: 0.7887 (tptt) REVERT: B 93 TYR cc_start: 0.6635 (m-80) cc_final: 0.6157 (m-80) REVERT: B 159 SER cc_start: 0.7840 (OUTLIER) cc_final: 0.7490 (p) REVERT: B 189 ILE cc_start: 0.8700 (mm) cc_final: 0.8407 (mm) REVERT: B 197 TYR cc_start: 0.7010 (m-80) cc_final: 0.6658 (m-80) REVERT: B 221 MET cc_start: 0.7163 (mtt) cc_final: 0.6875 (mtt) outliers start: 40 outliers final: 23 residues processed: 226 average time/residue: 0.2666 time to fit residues: 76.6087 Evaluate side-chains 221 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 6703 Z= 0.362 Angle : 0.767 7.695 9118 Z= 0.404 Chirality : 0.049 0.155 1003 Planarity : 0.006 0.062 1175 Dihedral : 7.492 81.041 934 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.87 % Favored : 86.01 % Rotamer: Outliers : 5.85 % Allowed : 19.22 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.27), residues: 815 helix: -2.38 (1.00), residues: 17 sheet: -2.53 (0.33), residues: 213 loop : -2.65 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.004 TRP B 174 HIS 0.006 0.002 HIS A 66 PHE 0.048 0.003 PHE A 55 TYR 0.015 0.002 TYR A 37 ARG 0.008 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 212 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7676 (tm130) cc_final: 0.7451 (tp40) REVERT: A 67 VAL cc_start: 0.8857 (p) cc_final: 0.8414 (m) REVERT: A 170 TYR cc_start: 0.8828 (t80) cc_final: 0.8434 (t80) REVERT: A 177 MET cc_start: 0.6727 (mmt) cc_final: 0.6410 (mmt) REVERT: A 224 GLU cc_start: 0.7366 (pm20) cc_final: 0.6976 (pm20) REVERT: A 229 LEU cc_start: 0.8309 (tp) cc_final: 0.8082 (mm) REVERT: A 265 TYR cc_start: 0.6972 (m-80) cc_final: 0.6489 (m-80) REVERT: A 310 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8685 (mmmm) REVERT: A 355 ARG cc_start: 0.7877 (ttm-80) cc_final: 0.7367 (mtp85) REVERT: A 360 ASN cc_start: 0.8704 (OUTLIER) cc_final: 0.8488 (p0) REVERT: A 388 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7740 (t0) REVERT: A 408 ARG cc_start: 0.8094 (ttp-170) cc_final: 0.7749 (ttp-170) REVERT: A 417 ASN cc_start: 0.8139 (t0) cc_final: 0.7791 (t0) REVERT: A 424 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8182 (tptp) REVERT: A 425 LEU cc_start: 0.8800 (tp) cc_final: 0.8578 (tt) REVERT: A 442 ASP cc_start: 0.8135 (p0) cc_final: 0.7826 (p0) REVERT: A 452 LEU cc_start: 0.7773 (mp) cc_final: 0.7305 (tt) REVERT: A 490 PHE cc_start: 0.8059 (t80) cc_final: 0.7812 (t80) REVERT: A 501 TYR cc_start: 0.8062 (OUTLIER) cc_final: 0.7688 (t80) REVERT: A 588 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8697 (p) REVERT: A 606 ASN cc_start: 0.8521 (t0) cc_final: 0.8151 (t0) REVERT: B 29 PHE cc_start: 0.8163 (m-80) cc_final: 0.7568 (m-80) REVERT: B 64 LYS cc_start: 0.8407 (tptt) cc_final: 0.8057 (tptt) REVERT: B 78 LEU cc_start: 0.7906 (mm) cc_final: 0.7632 (mm) REVERT: B 93 TYR cc_start: 0.6688 (m-80) cc_final: 0.6150 (m-80) REVERT: B 110 GLN cc_start: 0.6217 (mp10) cc_final: 0.5994 (mp10) REVERT: B 172 MET cc_start: 0.6850 (mpt) cc_final: 0.6596 (mpt) REVERT: B 189 ILE cc_start: 0.8786 (mm) cc_final: 0.8451 (mm) REVERT: B 219 LEU cc_start: 0.8263 (tp) cc_final: 0.7602 (tp) REVERT: B 243 TYR cc_start: 0.7890 (t80) cc_final: 0.7585 (t80) outliers start: 42 outliers final: 25 residues processed: 234 average time/residue: 0.2318 time to fit residues: 68.8009 Evaluate side-chains 231 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 422 ASN Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 chunk 19 optimal weight: 7.9990 chunk 79 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 360 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.5768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6703 Z= 0.189 Angle : 0.716 9.169 9118 Z= 0.362 Chirality : 0.047 0.165 1003 Planarity : 0.005 0.060 1175 Dihedral : 6.865 81.689 930 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 4.04 % Allowed : 22.70 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.28), residues: 815 helix: -1.95 (1.18), residues: 17 sheet: -2.20 (0.35), residues: 207 loop : -2.54 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 174 HIS 0.005 0.001 HIS A 519 PHE 0.030 0.002 PHE A 55 TYR 0.018 0.001 TYR A 660 ARG 0.008 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7571 (tm130) cc_final: 0.7151 (tp40) REVERT: A 67 VAL cc_start: 0.8430 (p) cc_final: 0.7997 (m) REVERT: A 177 MET cc_start: 0.6467 (mmt) cc_final: 0.6171 (mmt) REVERT: A 224 GLU cc_start: 0.7238 (pm20) cc_final: 0.7025 (pm20) REVERT: A 241 LEU cc_start: 0.7795 (mm) cc_final: 0.7556 (mm) REVERT: A 265 TYR cc_start: 0.6710 (m-80) cc_final: 0.6230 (m-80) REVERT: A 313 TYR cc_start: 0.6379 (m-80) cc_final: 0.5730 (m-80) REVERT: A 337 PRO cc_start: 0.7912 (Cg_exo) cc_final: 0.7630 (Cg_endo) REVERT: A 355 ARG cc_start: 0.7726 (ttm-80) cc_final: 0.7524 (mtp85) REVERT: A 360 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8434 (p0) REVERT: A 388 ASN cc_start: 0.8127 (p0) cc_final: 0.7681 (t0) REVERT: A 408 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7240 (ttp-170) REVERT: A 414 GLN cc_start: 0.7559 (mm110) cc_final: 0.6867 (mp10) REVERT: A 417 ASN cc_start: 0.7946 (t0) cc_final: 0.7595 (t0) REVERT: A 424 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7883 (tptp) REVERT: A 442 ASP cc_start: 0.8257 (p0) cc_final: 0.7866 (p0) REVERT: A 501 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7598 (t80) REVERT: A 547 LYS cc_start: 0.7447 (mmmt) cc_final: 0.7019 (mmmt) REVERT: A 578 ASP cc_start: 0.8395 (t0) cc_final: 0.8179 (t0) REVERT: A 588 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8558 (p) REVERT: A 606 ASN cc_start: 0.8543 (t0) cc_final: 0.8182 (t0) REVERT: A 659 SER cc_start: 0.7687 (m) cc_final: 0.7240 (t) REVERT: B 29 PHE cc_start: 0.8089 (m-80) cc_final: 0.7547 (m-80) REVERT: B 38 ARG cc_start: 0.7581 (ttp80) cc_final: 0.7218 (ttp80) REVERT: B 64 LYS cc_start: 0.8191 (tptt) cc_final: 0.7890 (tptt) REVERT: B 93 TYR cc_start: 0.6365 (m-80) cc_final: 0.5859 (m-80) REVERT: B 110 GLN cc_start: 0.6258 (mp10) cc_final: 0.5993 (mp10) REVERT: B 159 SER cc_start: 0.7582 (m) cc_final: 0.7340 (t) REVERT: B 189 ILE cc_start: 0.8645 (mm) cc_final: 0.8370 (mm) REVERT: B 243 TYR cc_start: 0.7860 (t80) cc_final: 0.7618 (t80) outliers start: 29 outliers final: 22 residues processed: 225 average time/residue: 0.2278 time to fit residues: 64.4725 Evaluate side-chains 226 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 9.9990 chunk 45 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.6154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6703 Z= 0.272 Angle : 0.756 9.950 9118 Z= 0.383 Chirality : 0.049 0.271 1003 Planarity : 0.005 0.057 1175 Dihedral : 7.093 81.886 930 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.74 % Favored : 86.26 % Rotamer: Outliers : 5.29 % Allowed : 23.82 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.28), residues: 815 helix: -2.32 (1.04), residues: 17 sheet: -2.30 (0.35), residues: 211 loop : -2.41 (0.24), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP B 174 HIS 0.006 0.002 HIS A 519 PHE 0.027 0.002 PHE A 275 TYR 0.017 0.002 TYR A 660 ARG 0.009 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 VAL cc_start: 0.8610 (p) cc_final: 0.8198 (m) REVERT: A 86 PHE cc_start: 0.8678 (t80) cc_final: 0.8204 (t80) REVERT: A 177 MET cc_start: 0.6766 (mmt) cc_final: 0.6472 (mmt) REVERT: A 224 GLU cc_start: 0.7287 (pm20) cc_final: 0.7081 (pm20) REVERT: A 229 LEU cc_start: 0.8338 (tp) cc_final: 0.8095 (mm) REVERT: A 265 TYR cc_start: 0.6804 (m-80) cc_final: 0.6340 (m-80) REVERT: A 313 TYR cc_start: 0.6657 (m-80) cc_final: 0.5998 (m-80) REVERT: A 328 ARG cc_start: 0.6749 (ttm110) cc_final: 0.6490 (ttm110) REVERT: A 360 ASN cc_start: 0.8672 (p0) cc_final: 0.8447 (p0) REVERT: A 388 ASN cc_start: 0.8183 (p0) cc_final: 0.7751 (t0) REVERT: A 408 ARG cc_start: 0.8003 (ttp-170) cc_final: 0.7679 (ttp-170) REVERT: A 417 ASN cc_start: 0.8122 (t0) cc_final: 0.7783 (t0) REVERT: A 424 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8079 (tptt) REVERT: A 442 ASP cc_start: 0.8205 (p0) cc_final: 0.7866 (p0) REVERT: A 501 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7675 (t80) REVERT: A 588 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8658 (p) REVERT: A 606 ASN cc_start: 0.8520 (t0) cc_final: 0.8148 (t0) REVERT: A 659 SER cc_start: 0.7806 (m) cc_final: 0.7400 (t) REVERT: B 29 PHE cc_start: 0.8094 (m-80) cc_final: 0.7537 (m-80) REVERT: B 36 TRP cc_start: 0.6134 (m100) cc_final: 0.5893 (m100) REVERT: B 64 LYS cc_start: 0.8250 (tptt) cc_final: 0.7952 (tptt) REVERT: B 93 TYR cc_start: 0.6596 (m-80) cc_final: 0.6352 (m-80) REVERT: B 110 GLN cc_start: 0.6161 (mp10) cc_final: 0.5956 (mp10) REVERT: B 189 ILE cc_start: 0.8648 (mm) cc_final: 0.8286 (mm) outliers start: 38 outliers final: 30 residues processed: 225 average time/residue: 0.2414 time to fit residues: 68.2750 Evaluate side-chains 238 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 205 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.6382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6703 Z= 0.247 Angle : 0.784 11.137 9118 Z= 0.396 Chirality : 0.048 0.240 1003 Planarity : 0.006 0.090 1175 Dihedral : 6.994 82.099 930 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 5.15 % Allowed : 24.37 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.28), residues: 815 helix: -2.44 (0.92), residues: 22 sheet: -2.20 (0.35), residues: 209 loop : -2.36 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP B 174 HIS 0.003 0.001 HIS A 519 PHE 0.032 0.002 PHE A 275 TYR 0.016 0.001 TYR A 660 ARG 0.007 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7577 (tp40) cc_final: 0.7202 (tp40) REVERT: A 86 PHE cc_start: 0.8620 (t80) cc_final: 0.8368 (t80) REVERT: A 177 MET cc_start: 0.6915 (mmt) cc_final: 0.6498 (mmt) REVERT: A 224 GLU cc_start: 0.7286 (pm20) cc_final: 0.6983 (pm20) REVERT: A 313 TYR cc_start: 0.6592 (m-80) cc_final: 0.5931 (m-80) REVERT: A 357 ARG cc_start: 0.8016 (mtp-110) cc_final: 0.7795 (mtp-110) REVERT: A 360 ASN cc_start: 0.8636 (p0) cc_final: 0.8385 (p0) REVERT: A 388 ASN cc_start: 0.8130 (p0) cc_final: 0.7729 (t0) REVERT: A 408 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7657 (ttp-170) REVERT: A 417 ASN cc_start: 0.8042 (t0) cc_final: 0.7692 (t0) REVERT: A 424 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7884 (tptt) REVERT: A 442 ASP cc_start: 0.8279 (p0) cc_final: 0.7920 (p0) REVERT: A 501 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7622 (t80) REVERT: A 547 LYS cc_start: 0.7438 (mmmt) cc_final: 0.6987 (mmmt) REVERT: A 577 ARG cc_start: 0.7557 (tpt170) cc_final: 0.7126 (tpm170) REVERT: A 588 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8601 (p) REVERT: A 642 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8285 (t) REVERT: A 659 SER cc_start: 0.7755 (m) cc_final: 0.7140 (t) REVERT: B 29 PHE cc_start: 0.8082 (m-80) cc_final: 0.7535 (m-80) REVERT: B 64 LYS cc_start: 0.8197 (tptt) cc_final: 0.7927 (tptt) REVERT: B 82 MET cc_start: 0.8601 (mtt) cc_final: 0.8228 (ttt) REVERT: B 189 ILE cc_start: 0.8575 (mm) cc_final: 0.8296 (mm) REVERT: B 197 TYR cc_start: 0.7508 (m-80) cc_final: 0.7300 (m-80) REVERT: B 243 TYR cc_start: 0.7617 (t80) cc_final: 0.7369 (t80) outliers start: 37 outliers final: 30 residues processed: 234 average time/residue: 0.2320 time to fit residues: 68.3108 Evaluate side-chains 244 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 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 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.6545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6703 Z= 0.227 Angle : 0.801 12.365 9118 Z= 0.405 Chirality : 0.048 0.234 1003 Planarity : 0.005 0.059 1175 Dihedral : 6.815 81.776 930 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 4.74 % Allowed : 25.63 % Favored : 69.64 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.28), residues: 815 helix: -2.34 (0.97), residues: 22 sheet: -2.19 (0.35), residues: 213 loop : -2.31 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.003 TRP B 174 HIS 0.006 0.002 HIS A 519 PHE 0.021 0.002 PHE B 206 TYR 0.015 0.002 TYR A 660 ARG 0.012 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7431 (tp40) cc_final: 0.7024 (tp40) REVERT: A 177 MET cc_start: 0.7141 (mmt) cc_final: 0.6813 (mmt) REVERT: A 313 TYR cc_start: 0.6575 (m-80) cc_final: 0.5906 (m-80) REVERT: A 355 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7687 (mtp85) REVERT: A 357 ARG cc_start: 0.8082 (mtp-110) cc_final: 0.7851 (mtp-110) REVERT: A 360 ASN cc_start: 0.8618 (p0) cc_final: 0.8390 (p0) REVERT: A 388 ASN cc_start: 0.8119 (p0) cc_final: 0.7727 (t0) REVERT: A 408 ARG cc_start: 0.7976 (ttp-170) cc_final: 0.7653 (ttp-170) REVERT: A 417 ASN cc_start: 0.7984 (t0) cc_final: 0.7621 (t0) REVERT: A 442 ASP cc_start: 0.8267 (p0) cc_final: 0.7925 (p0) REVERT: A 501 TYR cc_start: 0.7999 (OUTLIER) cc_final: 0.7592 (t80) REVERT: A 547 LYS cc_start: 0.7438 (mmmt) cc_final: 0.7020 (mmmt) REVERT: A 562 PHE cc_start: 0.6888 (t80) cc_final: 0.6658 (t80) REVERT: A 588 THR cc_start: 0.8724 (OUTLIER) cc_final: 0.8522 (p) REVERT: A 642 VAL cc_start: 0.8576 (OUTLIER) cc_final: 0.8321 (t) REVERT: A 643 PHE cc_start: 0.6654 (t80) cc_final: 0.6346 (t80) REVERT: A 659 SER cc_start: 0.7289 (m) cc_final: 0.7018 (t) REVERT: A 673 SER cc_start: 0.8735 (t) cc_final: 0.8284 (m) REVERT: B 29 PHE cc_start: 0.8071 (m-80) cc_final: 0.7519 (m-80) REVERT: B 64 LYS cc_start: 0.8173 (tptt) cc_final: 0.7915 (tptt) REVERT: B 82 MET cc_start: 0.8504 (mtt) cc_final: 0.8281 (ttt) REVERT: B 157 ARG cc_start: 0.7903 (ttt90) cc_final: 0.7678 (ttt90) REVERT: B 165 PHE cc_start: 0.7851 (t80) cc_final: 0.7586 (t80) REVERT: B 189 ILE cc_start: 0.8549 (mm) cc_final: 0.8248 (mm) REVERT: B 192 LEU cc_start: 0.8126 (pt) cc_final: 0.7664 (tp) REVERT: B 217 LEU cc_start: 0.8499 (tt) cc_final: 0.8010 (mp) REVERT: B 243 TYR cc_start: 0.7673 (t80) cc_final: 0.7401 (t80) outliers start: 34 outliers final: 26 residues processed: 229 average time/residue: 0.2340 time to fit residues: 67.3503 Evaluate side-chains 229 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 471 GLU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 0.0370 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 606 ASN A 675 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6703 Z= 0.219 Angle : 0.829 13.052 9118 Z= 0.415 Chirality : 0.049 0.242 1003 Planarity : 0.006 0.070 1175 Dihedral : 6.744 81.756 928 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 3.76 % Allowed : 28.97 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.21 (0.28), residues: 815 helix: -2.33 (1.01), residues: 22 sheet: -2.01 (0.36), residues: 211 loop : -2.32 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.004 TRP B 174 HIS 0.005 0.001 HIS A 519 PHE 0.024 0.002 PHE B 206 TYR 0.021 0.001 TYR A 91 ARG 0.007 0.001 ARG B 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1630 Ramachandran restraints generated. 815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.7385 (tp40) cc_final: 0.7020 (tp40) REVERT: A 177 MET cc_start: 0.7100 (mmt) cc_final: 0.6782 (mmt) REVERT: A 229 LEU cc_start: 0.8249 (tp) cc_final: 0.8048 (mm) REVERT: A 313 TYR cc_start: 0.6472 (m-80) cc_final: 0.5827 (m-80) REVERT: A 355 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7669 (mtp85) REVERT: A 357 ARG cc_start: 0.8049 (mtp-110) cc_final: 0.7844 (mtp-110) REVERT: A 360 ASN cc_start: 0.8641 (p0) cc_final: 0.8425 (p0) REVERT: A 388 ASN cc_start: 0.8077 (p0) cc_final: 0.7646 (t0) REVERT: A 408 ARG cc_start: 0.7989 (ttp-170) cc_final: 0.7649 (ttp-170) REVERT: A 417 ASN cc_start: 0.7977 (t0) cc_final: 0.7595 (t0) REVERT: A 442 ASP cc_start: 0.8285 (p0) cc_final: 0.7915 (p0) REVERT: A 501 TYR cc_start: 0.7996 (OUTLIER) cc_final: 0.7585 (t80) REVERT: A 515 PHE cc_start: 0.7195 (m-80) cc_final: 0.6938 (m-80) REVERT: A 642 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8352 (t) REVERT: A 643 PHE cc_start: 0.6659 (t80) cc_final: 0.6339 (t80) REVERT: B 29 PHE cc_start: 0.8052 (m-80) cc_final: 0.7520 (m-80) REVERT: B 64 LYS cc_start: 0.8143 (tptt) cc_final: 0.7888 (tptt) REVERT: B 156 LEU cc_start: 0.8074 (tp) cc_final: 0.7672 (tp) REVERT: B 189 ILE cc_start: 0.8445 (mm) cc_final: 0.8168 (mm) REVERT: B 192 LEU cc_start: 0.8137 (pt) cc_final: 0.7546 (tp) REVERT: B 217 LEU cc_start: 0.8439 (tt) cc_final: 0.7995 (mp) outliers start: 27 outliers final: 22 residues processed: 214 average time/residue: 0.2371 time to fit residues: 63.2270 Evaluate side-chains 222 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 41 LYS Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 606 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain B residue 1 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 27 optimal weight: 0.3980 chunk 66 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.162274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.130438 restraints weight = 12580.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.136030 restraints weight = 7327.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.139839 restraints weight = 4878.669| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.160 6703 Z= 0.378 Angle : 1.198 59.188 9118 Z= 0.671 Chirality : 0.063 1.147 1003 Planarity : 0.006 0.070 1175 Dihedral : 6.739 81.759 928 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.27 % Favored : 87.73 % Rotamer: Outliers : 3.20 % Allowed : 29.39 % Favored : 67.41 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.28), residues: 815 helix: -2.35 (1.01), residues: 22 sheet: -2.00 (0.36), residues: 211 loop : -2.33 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.004 TRP B 174 HIS 0.003 0.001 HIS A 66 PHE 0.015 0.002 PHE A 55 TYR 0.029 0.002 TYR A 269 ARG 0.007 0.001 ARG A 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.88 seconds wall clock time: 39 minutes 55.87 seconds (2395.87 seconds total)