Starting phenix.real_space_refine on Mon Mar 11 01:33:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/03_2024/8i4h_35173.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/03_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_35173/03_2024/8i4h_35173.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/03_2024/8i4h_35173.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/03_2024/8i4h_35173.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4h_35173/03_2024/8i4h_35173.pdb" } 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 Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" 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: 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: 4.07, per 1000 atoms: 0.62 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 - 3.50 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: 2.36 Conformation dependent library (CDL) restraints added in 1.4 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: 0.88 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: 1.87 Time building geometry restraints manager: 2.61 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: 100.82 - 107.45: 225 107.45 - 114.08: 3644 114.08 - 120.71: 2502 120.71 - 127.33: 2687 127.33 - 133.96: 60 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 2.440 nonbonded pdb=" O VAL A 130 " pdb=" OG1 THR A 167 " model vdw 2.270 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.275 2.440 nonbonded pdb=" OG1 THR A 470 " pdb=" OG SER B 54 " model vdw 2.277 2.440 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.295 2.440 ... (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 ========== 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.990 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.910 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.300 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 42 poor density : 246 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: 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: 0.2107 time to fit residues: 72.0306 Evaluate side-chains 218 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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: 5.9990 chunk 34 optimal weight: 0.0000 chunk 21 optimal weight: 0.4980 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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 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 13 GLN B 81 GLN B 110 GLN B 141 GLN B 212 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6703 Z= 0.212 Angle : 0.611 7.546 9118 Z= 0.309 Chirality : 0.045 0.241 1003 Planarity : 0.004 0.054 1175 Dihedral : 6.450 82.493 950 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.92 % Favored : 89.08 % Rotamer: Outliers : 5.99 % Allowed : 14.21 % Favored : 79.81 % 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: -4.11 (0.26), residues: 815 helix: -2.35 (1.17), residues: 16 sheet: -2.74 (0.34), residues: 195 loop : -2.96 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 174 HIS 0.018 0.003 HIS A 519 PHE 0.033 0.001 PHE A 306 TYR 0.010 0.001 TYR A 160 ARG 0.002 0.000 ARG A 273 *********************** 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 266 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 0.756 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: A 52 GLN cc_start: 0.7734 (tm-30) cc_final: 0.7346 (tp40) REVERT: A 92 PHE cc_start: 0.6464 (t80) cc_final: 0.6110 (t80) REVERT: A 100 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9074 (tp) REVERT: A 177 MET cc_start: 0.6171 (mmt) cc_final: 0.5883 (mmt) REVERT: A 204 LYS cc_start: 0.8203 (tttp) cc_final: 0.7978 (tttp) REVERT: A 357 ARG cc_start: 0.7094 (ttp80) cc_final: 0.6722 (ttp80) REVERT: A 359 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7714 (t) REVERT: A 368 LEU cc_start: 0.8112 (mm) cc_final: 0.7569 (tp) REVERT: A 387 LEU cc_start: 0.8684 (mt) cc_final: 0.8322 (tp) REVERT: A 396 TYR cc_start: 0.6989 (m-80) cc_final: 0.6439 (m-10) REVERT: A 408 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7598 (ttp-170) REVERT: A 417 ASN cc_start: 0.7845 (t0) cc_final: 0.7455 (t0) REVERT: A 424 LYS cc_start: 0.8164 (tmtm) cc_final: 0.7825 (tmtm) REVERT: A 452 LEU cc_start: 0.7763 (mp) cc_final: 0.7274 (tt) REVERT: A 501 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.7288 (t80) REVERT: A 528 LYS cc_start: 0.7514 (mttm) cc_final: 0.6953 (mttp) REVERT: A 537 LYS cc_start: 0.7899 (tppp) cc_final: 0.7456 (mmmm) REVERT: A 564 GLN cc_start: 0.7556 (pp30) cc_final: 0.7302 (tm-30) REVERT: A 588 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8626 (p) REVERT: A 598 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8169 (tp) REVERT: A 664 ILE cc_start: 0.8771 (pt) cc_final: 0.8467 (pt) REVERT: B 38 ARG cc_start: 0.7212 (ttp-170) cc_final: 0.6761 (ttp-170) REVERT: B 45 PRO cc_start: 0.8806 (Cg_endo) cc_final: 0.8539 (Cg_exo) REVERT: B 51 MET cc_start: 0.8098 (tpt) cc_final: 0.7840 (tpt) REVERT: B 64 LYS cc_start: 0.8051 (tptt) cc_final: 0.7816 (mptt) REVERT: B 93 TYR cc_start: 0.6603 (m-80) cc_final: 0.5601 (m-80) REVERT: B 189 ILE cc_start: 0.8679 (mm) cc_final: 0.8399 (mm) REVERT: B 252 THR cc_start: 0.8472 (t) cc_final: 0.8200 (m) outliers start: 43 outliers final: 22 residues processed: 247 average time/residue: 0.2286 time to fit residues: 70.6294 Evaluate side-chains 226 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 308 VAL 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 143 VAL Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 234 ASN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 580 GLN A 690 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 6703 Z= 0.404 Angle : 0.773 9.099 9118 Z= 0.407 Chirality : 0.048 0.158 1003 Planarity : 0.005 0.060 1175 Dihedral : 7.598 81.745 942 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 26.37 Ramachandran Plot: Outliers : 0.12 % Allowed : 13.87 % Favored : 86.01 % Rotamer: Outliers : 6.55 % Allowed : 17.69 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -3.90 (0.27), residues: 815 helix: -1.29 (1.39), residues: 16 sheet: -2.74 (0.35), residues: 193 loop : -2.78 (0.23), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP B 174 HIS 0.018 0.004 HIS A 519 PHE 0.040 0.003 PHE A 275 TYR 0.019 0.002 TYR A 37 ARG 0.005 0.001 ARG A 346 *********************** 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 275 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 228 time to evaluate : 0.659 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 84 LEU cc_start: 0.8713 (mt) cc_final: 0.8451 (mt) REVERT: A 86 PHE cc_start: 0.8650 (t80) cc_final: 0.8279 (t80) REVERT: A 100 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9107 (tp) REVERT: A 170 TYR cc_start: 0.8822 (t80) cc_final: 0.8427 (t80) REVERT: A 177 MET cc_start: 0.6507 (mmt) cc_final: 0.6177 (mmt) REVERT: A 265 TYR cc_start: 0.6968 (m-80) cc_final: 0.6704 (m-80) REVERT: A 304 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8339 (mmtp) REVERT: A 328 ARG cc_start: 0.6587 (ttm110) cc_final: 0.6315 (ttm110) REVERT: A 360 ASN cc_start: 0.8633 (p0) cc_final: 0.8304 (p0) REVERT: A 367 VAL cc_start: 0.8148 (m) cc_final: 0.7906 (p) REVERT: A 368 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8092 (tt) REVERT: A 387 LEU cc_start: 0.8716 (mt) cc_final: 0.8497 (tp) REVERT: A 396 TYR cc_start: 0.7040 (m-80) cc_final: 0.5943 (m-10) REVERT: A 408 ARG cc_start: 0.8146 (ttp-170) cc_final: 0.7799 (ttp-170) REVERT: A 417 ASN cc_start: 0.8169 (t0) cc_final: 0.7822 (t0) REVERT: A 424 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8220 (tptp) REVERT: A 442 ASP cc_start: 0.8155 (p0) cc_final: 0.7872 (p0) REVERT: A 452 LEU cc_start: 0.7836 (mp) cc_final: 0.7258 (tt) REVERT: A 462 LYS cc_start: 0.8372 (tptp) cc_final: 0.8128 (tptp) REVERT: A 465 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6488 (mm-30) REVERT: A 501 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7625 (t80) REVERT: A 537 LYS cc_start: 0.8213 (tppp) cc_final: 0.7607 (mmmm) REVERT: A 562 PHE cc_start: 0.7044 (t80) cc_final: 0.6840 (t80) REVERT: A 598 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8198 (tp) REVERT: A 607 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8181 (mm-40) REVERT: A 674 TYR cc_start: 0.8420 (t80) cc_final: 0.8183 (t80) REVERT: B 29 PHE cc_start: 0.8078 (m-80) cc_final: 0.7418 (m-80) REVERT: B 64 LYS cc_start: 0.8267 (tptt) cc_final: 0.8005 (tptt) REVERT: B 78 LEU cc_start: 0.7565 (mm) cc_final: 0.7237 (mm) REVERT: B 93 TYR cc_start: 0.6503 (m-80) cc_final: 0.5827 (m-80) REVERT: B 107 TYR cc_start: 0.6634 (t80) cc_final: 0.6373 (t80) REVERT: B 110 GLN cc_start: 0.6549 (mp10) cc_final: 0.6277 (mp10) REVERT: B 159 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.7983 (t) REVERT: B 189 ILE cc_start: 0.8837 (mm) cc_final: 0.8481 (mm) REVERT: B 207 THR cc_start: 0.7623 (OUTLIER) cc_final: 0.7338 (t) REVERT: B 219 LEU cc_start: 0.8475 (tp) cc_final: 0.7240 (tp) REVERT: B 252 THR cc_start: 0.8082 (t) cc_final: 0.7852 (m) REVERT: B 254 VAL cc_start: 0.9022 (m) cc_final: 0.8788 (p) outliers start: 47 outliers final: 28 residues processed: 252 average time/residue: 0.2392 time to fit residues: 75.5626 Evaluate side-chains 241 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR 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 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 241 LEU 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 368 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR 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 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 58 TYR 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 207 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- 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 321 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6703 Z= 0.207 Angle : 0.700 11.654 9118 Z= 0.349 Chirality : 0.046 0.248 1003 Planarity : 0.005 0.058 1175 Dihedral : 7.334 82.126 940 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 6.82 % Allowed : 19.92 % 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: -3.57 (0.27), residues: 815 helix: -0.87 (1.39), residues: 16 sheet: -2.44 (0.36), residues: 189 loop : -2.58 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B 174 HIS 0.003 0.001 HIS A 519 PHE 0.036 0.002 PHE A 275 TYR 0.013 0.001 TYR B 243 ARG 0.005 0.001 ARG A 346 *********************** 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 255 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 206 time to evaluate : 0.656 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: 0.7804 (tp40) cc_final: 0.7544 (tp40) REVERT: A 86 PHE cc_start: 0.8594 (t80) cc_final: 0.8302 (t80) REVERT: A 100 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9140 (tp) REVERT: A 177 MET cc_start: 0.6418 (mmt) cc_final: 0.6110 (mmt) REVERT: A 224 GLU cc_start: 0.7436 (pm20) cc_final: 0.7024 (pm20) REVERT: A 313 TYR cc_start: 0.6472 (m-80) cc_final: 0.5887 (m-80) REVERT: A 328 ARG cc_start: 0.6415 (ttm110) cc_final: 0.5989 (ttm110) REVERT: A 355 ARG cc_start: 0.7998 (mtp85) cc_final: 0.7644 (mtp85) REVERT: A 360 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8382 (p0) REVERT: A 387 LEU cc_start: 0.8658 (mt) cc_final: 0.8424 (tp) REVERT: A 390 LEU cc_start: 0.8247 (tp) cc_final: 0.7824 (pt) REVERT: A 395 VAL cc_start: 0.7910 (m) cc_final: 0.7609 (t) REVERT: A 408 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7638 (ttp-170) REVERT: A 417 ASN cc_start: 0.8056 (t0) cc_final: 0.7733 (t0) REVERT: A 424 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8147 (tptp) REVERT: A 442 ASP cc_start: 0.8275 (p0) cc_final: 0.7902 (p0) REVERT: A 501 TYR cc_start: 0.8048 (OUTLIER) cc_final: 0.7570 (t80) REVERT: A 588 THR cc_start: 0.8927 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 591 SER cc_start: 0.7756 (m) cc_final: 0.7452 (p) REVERT: A 606 ASN cc_start: 0.8336 (p0) cc_final: 0.8120 (p0) REVERT: B 29 PHE cc_start: 0.8048 (m-80) cc_final: 0.7430 (m-80) REVERT: B 64 LYS cc_start: 0.8228 (tptt) cc_final: 0.7883 (tptt) REVERT: B 78 LEU cc_start: 0.7419 (mm) cc_final: 0.7070 (mm) REVERT: B 93 TYR cc_start: 0.6096 (m-80) cc_final: 0.5709 (m-80) REVERT: B 189 ILE cc_start: 0.8737 (mm) cc_final: 0.8369 (mm) REVERT: B 215 ASN cc_start: 0.8873 (t0) cc_final: 0.8649 (t0) REVERT: B 219 LEU cc_start: 0.8419 (tp) cc_final: 0.7619 (tp) REVERT: B 243 TYR cc_start: 0.7784 (t80) cc_final: 0.7230 (t80) REVERT: B 245 PHE cc_start: 0.7027 (m-80) cc_final: 0.6820 (m-80) REVERT: B 252 THR cc_start: 0.8151 (t) cc_final: 0.7926 (m) outliers start: 49 outliers final: 27 residues processed: 231 average time/residue: 0.2191 time to fit residues: 64.5661 Evaluate side-chains 230 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 198 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 83 VAL 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 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 360 ASN 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 399 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 470 THR 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 588 THR 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 44 THR Chi-restraints excluded: chain B residue 60 ASN 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 231 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 422 ASN A 505 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 564 GLN A 580 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6703 Z= 0.199 Angle : 0.713 10.114 9118 Z= 0.355 Chirality : 0.046 0.224 1003 Planarity : 0.005 0.062 1175 Dihedral : 7.261 81.049 936 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 6.13 % Allowed : 22.42 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.46 (0.27), residues: 815 helix: -1.26 (1.31), residues: 18 sheet: -2.31 (0.36), residues: 187 loop : -2.52 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 174 HIS 0.010 0.002 HIS A 519 PHE 0.045 0.002 PHE A 55 TYR 0.013 0.001 TYR A 660 ARG 0.007 0.001 ARG B 38 *********************** 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 256 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 212 time to evaluate : 0.652 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: A 52 GLN cc_start: 0.7788 (tp40) cc_final: 0.7521 (tp40) REVERT: A 86 PHE cc_start: 0.8575 (t80) cc_final: 0.8277 (t80) REVERT: A 100 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9105 (tp) REVERT: A 177 MET cc_start: 0.6471 (mmt) cc_final: 0.6162 (mmt) REVERT: A 310 LYS cc_start: 0.8694 (mppt) cc_final: 0.8458 (mmmm) REVERT: A 313 TYR cc_start: 0.6387 (m-80) cc_final: 0.5801 (m-80) REVERT: A 328 ARG cc_start: 0.6134 (ttm110) cc_final: 0.5825 (ttm110) REVERT: A 355 ARG cc_start: 0.7961 (mtp85) cc_final: 0.7536 (mtp85) REVERT: A 360 ASN cc_start: 0.8667 (OUTLIER) cc_final: 0.8403 (p0) REVERT: A 390 LEU cc_start: 0.8260 (tp) cc_final: 0.7834 (pt) REVERT: A 395 VAL cc_start: 0.7913 (m) cc_final: 0.7607 (t) REVERT: A 408 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7544 (ttp-170) REVERT: A 417 ASN cc_start: 0.8011 (t0) cc_final: 0.7672 (t0) REVERT: A 424 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7862 (tptp) REVERT: A 442 ASP cc_start: 0.8329 (p0) cc_final: 0.7925 (p0) REVERT: A 501 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7417 (t80) REVERT: A 588 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8587 (p) REVERT: A 591 SER cc_start: 0.7667 (m) cc_final: 0.7413 (p) REVERT: A 602 THR cc_start: 0.8046 (t) cc_final: 0.7717 (p) REVERT: A 675 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8762 (mp10) REVERT: B 29 PHE cc_start: 0.8031 (m-80) cc_final: 0.7415 (m-80) REVERT: B 45 PRO cc_start: 0.8987 (Cg_endo) cc_final: 0.8767 (Cg_exo) REVERT: B 64 LYS cc_start: 0.8128 (tptt) cc_final: 0.7849 (tptt) REVERT: B 78 LEU cc_start: 0.7431 (mm) cc_final: 0.6687 (mm) REVERT: B 82 MET cc_start: 0.8601 (mtt) cc_final: 0.8287 (ttt) REVERT: B 172 MET cc_start: 0.6706 (mpt) cc_final: 0.6318 (mpt) REVERT: B 189 ILE cc_start: 0.8691 (mm) cc_final: 0.8339 (mm) REVERT: B 215 ASN cc_start: 0.8888 (t0) cc_final: 0.8667 (t0) REVERT: B 219 LEU cc_start: 0.8212 (tp) cc_final: 0.7844 (tp) REVERT: B 243 TYR cc_start: 0.7718 (t80) cc_final: 0.7419 (t80) REVERT: B 252 THR cc_start: 0.8231 (t) cc_final: 0.7937 (m) outliers start: 44 outliers final: 30 residues processed: 234 average time/residue: 0.2143 time to fit residues: 63.2378 Evaluate side-chains 235 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR 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 100 ILE Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 192 PHE 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 350 VAL 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 377 PHE Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU 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 569 ILE Chi-restraints excluded: chain A residue 588 THR 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 44 THR Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 208 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A 675 GLN ** B 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6703 Z= 0.330 Angle : 0.768 10.632 9118 Z= 0.396 Chirality : 0.048 0.238 1003 Planarity : 0.005 0.068 1175 Dihedral : 7.752 82.109 936 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 25.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.46 % Favored : 84.54 % Rotamer: Outliers : 7.38 % Allowed : 21.87 % Favored : 70.75 % 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: -3.34 (0.28), residues: 815 helix: -1.01 (1.34), residues: 17 sheet: -2.23 (0.35), residues: 206 loop : -2.41 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.004 TRP B 174 HIS 0.011 0.003 HIS A 519 PHE 0.018 0.002 PHE A 306 TYR 0.016 0.002 TYR A 660 ARG 0.008 0.001 ARG A 346 *********************** 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 262 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 209 time to evaluate : 0.717 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: 0.7890 (tp40) cc_final: 0.7508 (tp40) REVERT: A 86 PHE cc_start: 0.8674 (t80) cc_final: 0.8455 (t80) REVERT: A 100 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9107 (tp) REVERT: A 170 TYR cc_start: 0.8861 (t80) cc_final: 0.8496 (t80) REVERT: A 177 MET cc_start: 0.6849 (mmt) cc_final: 0.6533 (mmt) REVERT: A 310 LYS cc_start: 0.8871 (mppt) cc_final: 0.8666 (mmmm) REVERT: A 313 TYR cc_start: 0.6826 (m-80) cc_final: 0.6288 (m-80) REVERT: A 329 PHE cc_start: 0.6248 (t80) cc_final: 0.5773 (t80) REVERT: A 343 ASN cc_start: 0.8311 (t0) cc_final: 0.7878 (p0) REVERT: A 360 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8428 (p0) REVERT: A 377 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 401 VAL cc_start: 0.8144 (t) cc_final: 0.7805 (m) REVERT: A 408 ARG cc_start: 0.7988 (ttp-170) cc_final: 0.7688 (ttp-170) REVERT: A 417 ASN cc_start: 0.8239 (t0) cc_final: 0.7916 (t0) REVERT: A 424 LYS cc_start: 0.8473 (tmtm) cc_final: 0.8236 (tptp) REVERT: A 442 ASP cc_start: 0.8289 (p0) cc_final: 0.7937 (p0) REVERT: A 501 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.7589 (t80) REVERT: A 588 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8584 (p) REVERT: A 591 SER cc_start: 0.7930 (m) cc_final: 0.7684 (p) REVERT: A 656 VAL cc_start: 0.7733 (t) cc_final: 0.7487 (t) REVERT: A 695 TYR cc_start: 0.5528 (p90) cc_final: 0.5245 (p90) REVERT: B 29 PHE cc_start: 0.8072 (m-80) cc_final: 0.7525 (m-80) REVERT: B 64 LYS cc_start: 0.8349 (tptt) cc_final: 0.8043 (tptt) REVERT: B 82 MET cc_start: 0.8672 (mtt) cc_final: 0.8293 (ttt) REVERT: B 189 ILE cc_start: 0.8808 (mm) cc_final: 0.8516 (mt) REVERT: B 215 ASN cc_start: 0.8821 (t0) cc_final: 0.8575 (t0) REVERT: B 219 LEU cc_start: 0.8312 (tp) cc_final: 0.8000 (tp) REVERT: B 252 THR cc_start: 0.8218 (t) cc_final: 0.7891 (m) outliers start: 53 outliers final: 35 residues processed: 237 average time/residue: 0.2214 time to fit residues: 66.5299 Evaluate side-chains 238 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 198 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 100 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 241 LEU Chi-restraints excluded: chain A residue 271 GLN 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 377 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 470 THR 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 549 THR Chi-restraints excluded: chain A residue 588 THR 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 32 TYR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 60 ASN 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 212 ASN Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.6347 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= 0.249 Angle : 0.767 11.247 9118 Z= 0.383 Chirality : 0.048 0.244 1003 Planarity : 0.005 0.066 1175 Dihedral : 7.590 82.279 936 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.87 % Favored : 86.13 % Rotamer: Outliers : 6.82 % Allowed : 24.93 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.24 (0.28), residues: 815 helix: -0.95 (1.34), residues: 17 sheet: -2.13 (0.36), residues: 201 loop : -2.36 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP B 174 HIS 0.003 0.001 HIS A 519 PHE 0.017 0.002 PHE A 306 TYR 0.012 0.001 TYR A 660 ARG 0.006 0.001 ARG A 493 *********************** 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 259 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 210 time to evaluate : 0.642 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: A 52 GLN cc_start: 0.7766 (tp40) cc_final: 0.7391 (tp40) REVERT: A 86 PHE cc_start: 0.8652 (t80) cc_final: 0.8398 (t80) REVERT: A 177 MET cc_start: 0.6928 (mmt) cc_final: 0.6608 (mmt) REVERT: A 310 LYS cc_start: 0.8815 (mppt) cc_final: 0.8562 (mmmm) REVERT: A 313 TYR cc_start: 0.6797 (m-80) cc_final: 0.6115 (m-80) REVERT: A 343 ASN cc_start: 0.8309 (t0) cc_final: 0.7858 (p0) REVERT: A 355 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7276 (mtp85) REVERT: A 360 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8483 (p0) REVERT: A 377 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6805 (t80) REVERT: A 395 VAL cc_start: 0.7941 (m) cc_final: 0.7508 (t) REVERT: A 408 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.7630 (ttp-170) REVERT: A 417 ASN cc_start: 0.8141 (t0) cc_final: 0.7844 (t0) REVERT: A 424 LYS cc_start: 0.8287 (tmtm) cc_final: 0.8021 (tptp) REVERT: A 442 ASP cc_start: 0.8331 (p0) cc_final: 0.8017 (p0) REVERT: A 501 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7576 (t80) REVERT: A 588 THR cc_start: 0.8789 (OUTLIER) cc_final: 0.8560 (p) REVERT: A 591 SER cc_start: 0.7784 (m) cc_final: 0.7565 (p) REVERT: A 602 THR cc_start: 0.7809 (t) cc_final: 0.7408 (p) REVERT: A 643 PHE cc_start: 0.6752 (t80) cc_final: 0.6469 (t80) REVERT: A 656 VAL cc_start: 0.7662 (t) cc_final: 0.7459 (t) REVERT: A 695 TYR cc_start: 0.5381 (p90) cc_final: 0.5096 (p90) REVERT: B 29 PHE cc_start: 0.8018 (m-80) cc_final: 0.7492 (m-80) REVERT: B 82 MET cc_start: 0.8586 (mtt) cc_final: 0.8352 (ttt) REVERT: B 103 SER cc_start: 0.8327 (t) cc_final: 0.8127 (p) REVERT: B 156 LEU cc_start: 0.8021 (tp) cc_final: 0.7761 (tt) REVERT: B 189 ILE cc_start: 0.8740 (mm) cc_final: 0.8382 (mm) REVERT: B 215 ASN cc_start: 0.8829 (t0) cc_final: 0.8570 (t0) REVERT: B 252 THR cc_start: 0.8236 (t) cc_final: 0.7909 (m) outliers start: 49 outliers final: 38 residues processed: 233 average time/residue: 0.2119 time to fit residues: 62.0970 Evaluate side-chains 245 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 203 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 51 THR Chi-restraints excluded: chain A residue 78 ARG Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 100 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 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 271 GLN 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 377 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU 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 598 ILE 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 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 237 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 69 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** 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 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.6531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6703 Z= 0.238 Angle : 0.773 10.948 9118 Z= 0.389 Chirality : 0.048 0.254 1003 Planarity : 0.005 0.064 1175 Dihedral : 7.547 82.319 936 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer: Outliers : 6.27 % Allowed : 24.93 % Favored : 68.80 % 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: -3.20 (0.29), residues: 815 helix: -0.95 (1.33), residues: 17 sheet: -2.07 (0.36), residues: 209 loop : -2.33 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP B 174 HIS 0.004 0.001 HIS A 519 PHE 0.016 0.002 PHE A 65 TYR 0.015 0.001 TYR A 674 ARG 0.012 0.001 ARG A 577 *********************** 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 248 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 203 time to evaluate : 0.757 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: 0.7542 (tp40) cc_final: 0.7237 (tp40) REVERT: A 86 PHE cc_start: 0.8640 (t80) cc_final: 0.8411 (t80) REVERT: A 177 MET cc_start: 0.6964 (mmt) cc_final: 0.6629 (mmt) REVERT: A 313 TYR cc_start: 0.6807 (m-80) cc_final: 0.6129 (m-80) REVERT: A 328 ARG cc_start: 0.6597 (ttm110) cc_final: 0.5982 (ttm-80) REVERT: A 343 ASN cc_start: 0.8293 (t0) cc_final: 0.7846 (p0) REVERT: A 355 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7237 (mtp85) REVERT: A 359 SER cc_start: 0.8461 (m) cc_final: 0.8183 (t) REVERT: A 360 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8562 (p0) REVERT: A 377 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.6695 (t80) REVERT: A 395 VAL cc_start: 0.7905 (m) cc_final: 0.7479 (t) REVERT: A 408 ARG cc_start: 0.7920 (ttp-170) cc_final: 0.7621 (ttp-170) REVERT: A 417 ASN cc_start: 0.8219 (t0) cc_final: 0.7912 (t0) REVERT: A 424 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8123 (tptp) REVERT: A 442 ASP cc_start: 0.8394 (p0) cc_final: 0.8057 (p0) REVERT: A 501 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7583 (t80) REVERT: A 588 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8488 (p) REVERT: A 591 SER cc_start: 0.7755 (m) cc_final: 0.7550 (p) REVERT: A 602 THR cc_start: 0.7744 (t) cc_final: 0.7283 (p) REVERT: A 643 PHE cc_start: 0.6775 (t80) cc_final: 0.6489 (t80) REVERT: A 656 VAL cc_start: 0.7536 (t) cc_final: 0.7290 (t) REVERT: A 659 SER cc_start: 0.7771 (m) cc_final: 0.7271 (t) REVERT: A 695 TYR cc_start: 0.5385 (p90) cc_final: 0.4965 (p90) REVERT: B 29 PHE cc_start: 0.7973 (m-80) cc_final: 0.7466 (m-80) REVERT: B 66 LEU cc_start: 0.8735 (pt) cc_final: 0.8403 (pp) REVERT: B 189 ILE cc_start: 0.8669 (mm) cc_final: 0.8312 (mm) REVERT: B 215 ASN cc_start: 0.8831 (t0) cc_final: 0.8545 (t0) REVERT: B 252 THR cc_start: 0.8252 (t) cc_final: 0.7921 (m) outliers start: 45 outliers final: 36 residues processed: 223 average time/residue: 0.2266 time to fit residues: 63.4384 Evaluate side-chains 250 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 209 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 32 PHE 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 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 271 GLN 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 377 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 471 GLU 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 534 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 598 ILE 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 44 THR Chi-restraints excluded: chain B residue 60 ASN 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 212 ASN 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: 3.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.6864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6703 Z= 0.299 Angle : 0.807 11.849 9118 Z= 0.411 Chirality : 0.049 0.245 1003 Planarity : 0.005 0.060 1175 Dihedral : 7.730 82.972 934 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 26.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.95 % Favored : 84.05 % Rotamer: Outliers : 6.82 % Allowed : 24.93 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.26 (0.29), residues: 815 helix: -1.54 (1.10), residues: 23 sheet: -2.12 (0.35), residues: 209 loop : -2.36 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP B 174 HIS 0.009 0.002 HIS A 519 PHE 0.030 0.002 PHE A 562 TYR 0.016 0.002 TYR A 660 ARG 0.007 0.001 ARG A 493 *********************** 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 255 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 206 time to evaluate : 0.730 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: 0.7535 (tp40) cc_final: 0.7206 (tp40) REVERT: A 86 PHE cc_start: 0.8639 (t80) cc_final: 0.8420 (t80) REVERT: A 170 TYR cc_start: 0.9017 (t80) cc_final: 0.8588 (t80) REVERT: A 177 MET cc_start: 0.6923 (mmt) cc_final: 0.6621 (mmt) REVERT: A 310 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8502 (mmmm) REVERT: A 313 TYR cc_start: 0.6984 (m-80) cc_final: 0.6340 (m-80) REVERT: A 343 ASN cc_start: 0.8336 (t0) cc_final: 0.7878 (p0) REVERT: A 355 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7468 (mtp85) REVERT: A 359 SER cc_start: 0.8450 (m) cc_final: 0.8192 (t) REVERT: A 360 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8459 (p0) REVERT: A 377 PHE cc_start: 0.6661 (OUTLIER) cc_final: 0.6389 (t80) REVERT: A 395 VAL cc_start: 0.7923 (m) cc_final: 0.7467 (t) REVERT: A 408 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7682 (ttp-170) REVERT: A 417 ASN cc_start: 0.8316 (t0) cc_final: 0.8011 (t0) REVERT: A 424 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8187 (tptp) REVERT: A 442 ASP cc_start: 0.8353 (p0) cc_final: 0.8017 (p0) REVERT: A 501 TYR cc_start: 0.8057 (OUTLIER) cc_final: 0.7615 (t80) REVERT: A 588 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8533 (p) REVERT: A 591 SER cc_start: 0.7930 (m) cc_final: 0.7676 (p) REVERT: A 602 THR cc_start: 0.7768 (t) cc_final: 0.7371 (p) REVERT: A 643 PHE cc_start: 0.6857 (t80) cc_final: 0.6536 (t80) REVERT: A 656 VAL cc_start: 0.7698 (t) cc_final: 0.7454 (t) REVERT: A 659 SER cc_start: 0.7883 (m) cc_final: 0.7315 (t) REVERT: A 675 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8973 (mm-40) REVERT: A 695 TYR cc_start: 0.5337 (p90) cc_final: 0.4953 (p90) REVERT: B 29 PHE cc_start: 0.7988 (m-80) cc_final: 0.7454 (m-80) REVERT: B 66 LEU cc_start: 0.8697 (pt) cc_final: 0.8344 (pp) REVERT: B 189 ILE cc_start: 0.8681 (mm) cc_final: 0.8329 (mt) REVERT: B 198 TYR cc_start: 0.8007 (m-80) cc_final: 0.7799 (m-10) REVERT: B 215 ASN cc_start: 0.8807 (t0) cc_final: 0.8507 (t0) REVERT: B 252 THR cc_start: 0.8174 (t) cc_final: 0.7859 (m) outliers start: 49 outliers final: 36 residues processed: 229 average time/residue: 0.2233 time to fit residues: 64.3768 Evaluate side-chains 244 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 203 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 32 PHE 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 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 271 GLN 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 377 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 470 THR 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 588 THR Chi-restraints excluded: chain A residue 598 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 32 TYR Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 58 TYR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN A 580 GLN ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.7017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6703 Z= 0.266 Angle : 0.818 12.150 9118 Z= 0.414 Chirality : 0.048 0.255 1003 Planarity : 0.006 0.095 1175 Dihedral : 7.364 83.214 930 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 25.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.99 % Favored : 86.01 % Rotamer: Outliers : 5.85 % Allowed : 27.02 % Favored : 67.13 % 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: -3.26 (0.29), residues: 815 helix: -2.25 (0.92), residues: 29 sheet: -2.02 (0.35), residues: 223 loop : -2.35 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.004 TRP B 174 HIS 0.004 0.001 HIS A 519 PHE 0.027 0.002 PHE A 140 TYR 0.014 0.001 TYR A 660 ARG 0.007 0.001 ARG A 493 ********************** 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 243 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 0.908 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: 0.7562 (tp40) cc_final: 0.7253 (tp40) REVERT: A 105 ILE cc_start: 0.7330 (mt) cc_final: 0.7092 (mp) REVERT: A 170 TYR cc_start: 0.8989 (t80) cc_final: 0.8576 (t80) REVERT: A 313 TYR cc_start: 0.6959 (m-80) cc_final: 0.6286 (m-80) REVERT: A 343 ASN cc_start: 0.8331 (t0) cc_final: 0.7870 (p0) REVERT: A 346 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.6820 (pmt-80) REVERT: A 355 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7480 (mtp85) REVERT: A 359 SER cc_start: 0.8428 (m) cc_final: 0.8169 (t) REVERT: A 360 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8424 (p0) REVERT: A 377 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.6375 (t80) REVERT: A 395 VAL cc_start: 0.7863 (m) cc_final: 0.7417 (t) REVERT: A 408 ARG cc_start: 0.7946 (ttp-170) cc_final: 0.7658 (ttp-170) REVERT: A 417 ASN cc_start: 0.8286 (t0) cc_final: 0.7994 (t0) REVERT: A 424 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8188 (tptp) REVERT: A 442 ASP cc_start: 0.8386 (p0) cc_final: 0.7947 (p0) REVERT: A 501 TYR cc_start: 0.8024 (OUTLIER) cc_final: 0.7578 (t80) REVERT: A 588 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8470 (p) REVERT: A 591 SER cc_start: 0.7853 (m) cc_final: 0.7620 (p) REVERT: A 602 THR cc_start: 0.7681 (t) cc_final: 0.7192 (p) REVERT: A 643 PHE cc_start: 0.6774 (t80) cc_final: 0.6444 (t80) REVERT: A 656 VAL cc_start: 0.7711 (t) cc_final: 0.7468 (t) REVERT: A 659 SER cc_start: 0.7864 (m) cc_final: 0.7323 (t) REVERT: A 695 TYR cc_start: 0.5346 (p90) cc_final: 0.5016 (p90) REVERT: A 697 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7468 (ppp) REVERT: B 29 PHE cc_start: 0.7920 (m-80) cc_final: 0.7389 (m-80) REVERT: B 36 TRP cc_start: 0.5929 (m100) cc_final: 0.5696 (m100) REVERT: B 66 LEU cc_start: 0.8766 (pt) cc_final: 0.8399 (pp) REVERT: B 99 TRP cc_start: 0.7931 (OUTLIER) cc_final: 0.6475 (t60) REVERT: B 189 ILE cc_start: 0.8580 (mm) cc_final: 0.8336 (mt) REVERT: B 197 TYR cc_start: 0.7075 (m-80) cc_final: 0.6786 (m-80) REVERT: B 252 THR cc_start: 0.8200 (t) cc_final: 0.7901 (m) outliers start: 42 outliers final: 31 residues processed: 222 average time/residue: 0.2418 time to fit residues: 67.8068 Evaluate side-chains 241 residues out of total 726 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 32 PHE 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 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 271 GLN 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 377 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 424 LYS Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 470 THR 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 534 VAL Chi-restraints excluded: chain A residue 588 THR 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 44 THR Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 185 TRP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.0770 chunk 8 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 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 = 0.4228 r_free = 0.4228 target = 0.159263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.128445 restraints weight = 12710.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.133754 restraints weight = 7407.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.137484 restraints weight = 4974.262| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.7104 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= 0.240 Angle : 0.821 13.385 9118 Z= 0.409 Chirality : 0.048 0.253 1003 Planarity : 0.006 0.089 1175 Dihedral : 7.186 83.159 928 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 5.85 % Allowed : 26.88 % 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: -3.14 (0.29), residues: 815 helix: -2.31 (0.91), residues: 29 sheet: -1.92 (0.36), residues: 212 loop : -2.27 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP B 174 HIS 0.004 0.001 HIS A 519 PHE 0.025 0.002 PHE A 140 TYR 0.014 0.001 TYR A 660 ARG 0.007 0.001 ARG A 493 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.00 seconds wall clock time: 37 minutes 19.50 seconds (2239.50 seconds total)