Starting phenix.real_space_refine on Thu Sep 18 22:00:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h3i_0133/09_2025/6h3i_0133.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h3i_0133/09_2025/6h3i_0133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h3i_0133/09_2025/6h3i_0133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h3i_0133/09_2025/6h3i_0133.map" model { file = "/net/cci-nas-00/data/ceres_data/6h3i_0133/09_2025/6h3i_0133.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h3i_0133/09_2025/6h3i_0133.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.014 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: 5 Type Number sf(0) Gaussians S 46 5.16 5 C 12990 2.51 5 N 3461 2.21 5 O 4049 1.98 5 H 53 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20599 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 16848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2124, 16848 Classifications: {'peptide': 2124} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 97, 'TRANS': 2026} Chain breaks: 11 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1043 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2708 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 13, 'TRANS': 331} Chain breaks: 4 Time building chain proxies: 4.81, per 1000 atoms: 0.23 Number of scatterers: 20599 At special positions: 0 Unit cell: (117.26, 127.1, 135.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 O 4049 8.00 N 3461 7.00 C 12990 6.00 H 53 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 905.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4816 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 0 sheets defined 10.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 182 through 186 removed outlier: 3.906A pdb=" N THR A 185 " --> pdb=" O LYS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 306 removed outlier: 4.398A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 removed outlier: 3.709A pdb=" N GLU A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.261A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 413 removed outlier: 3.533A pdb=" N GLY A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.869A pdb=" N ASN A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 627 through 634 Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.686A pdb=" N MET A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 735 removed outlier: 3.534A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 819 Processing helix chain 'A' and resid 845 through 849 Processing helix chain 'A' and resid 914 through 920 removed outlier: 4.306A pdb=" N TYR A 918 " --> pdb=" O ASP A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 944 removed outlier: 3.896A pdb=" N LEU A 943 " --> pdb=" O TYR A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.547A pdb=" N ASN A 986 " --> pdb=" O PRO A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1081 through 1089 removed outlier: 4.267A pdb=" N ASN A1087 " --> pdb=" O ASP A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 4.272A pdb=" N TYR A1132 " --> pdb=" O VAL A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1426 through 1439 removed outlier: 3.995A pdb=" N LEU A1430 " --> pdb=" O ALA A1426 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ARG A1432 " --> pdb=" O ASP A1428 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER A1439 " --> pdb=" O ILE A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1576 Processing helix chain 'A' and resid 1607 through 1613 Processing helix chain 'A' and resid 1617 through 1622 Processing helix chain 'A' and resid 1856 through 1861 removed outlier: 3.647A pdb=" N SER A1860 " --> pdb=" O SER A1856 " (cutoff:3.500A) Processing helix chain 'A' and resid 1978 through 1982 Processing helix chain 'A' and resid 1989 through 1995 removed outlier: 3.705A pdb=" N GLY A1995 " --> pdb=" O ALA A1991 " (cutoff:3.500A) Processing helix chain 'A' and resid 2072 through 2076 removed outlier: 4.214A pdb=" N PHE A2076 " --> pdb=" O LYS A2073 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2104 removed outlier: 3.965A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2111 removed outlier: 3.521A pdb=" N VAL A2110 " --> pdb=" O GLY A2107 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA A2111 " --> pdb=" O SER A2108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2107 through 2111' Processing helix chain 'A' and resid 2129 through 2135 Processing helix chain 'A' and resid 2147 through 2152 removed outlier: 3.528A pdb=" N LEU A2151 " --> pdb=" O ASN A2147 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2161 Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 286 through 297 removed outlier: 4.225A pdb=" N TYR F 292 " --> pdb=" O ASP F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.764A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) 114 hydrogen bonds defined for protein. 291 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: 2.69 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 53 1.03 - 1.23: 244 1.23 - 1.42: 8887 1.42 - 1.62: 11763 1.62 - 1.81: 90 Bond restraints: 21037 Sorted by residual: bond pdb=" CD2 TYR A 309 " pdb=" CE2 TYR A 309 " ideal model delta sigma weight residual 1.382 1.310 0.072 3.00e-02 1.11e+03 5.83e+00 bond pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 1.512 1.467 0.045 2.20e-02 2.07e+03 4.10e+00 bond pdb=" C ASP A1600 " pdb=" N PRO A1601 " ideal model delta sigma weight residual 1.334 1.288 0.046 2.34e-02 1.83e+03 3.88e+00 bond pdb=" CB ILE A 990 " pdb=" CG2 ILE A 990 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.83e+00 bond pdb=" CB VAL A1345 " pdb=" CG1 VAL A1345 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.37e+00 ... (remaining 21032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 27821 2.50 - 5.00: 659 5.00 - 7.51: 69 7.51 - 10.01: 8 10.01 - 12.51: 1 Bond angle restraints: 28558 Sorted by residual: angle pdb=" N GLN F 58 " pdb=" CA GLN F 58 " pdb=" C GLN F 58 " ideal model delta sigma weight residual 114.04 107.91 6.13 1.24e+00 6.50e-01 2.44e+01 angle pdb=" C GLU A1035 " pdb=" N ILE A1036 " pdb=" CA ILE A1036 " ideal model delta sigma weight residual 120.49 126.64 -6.15 1.38e+00 5.25e-01 1.99e+01 angle pdb=" N ASN A 822 " pdb=" CA ASN A 822 " pdb=" C ASN A 822 " ideal model delta sigma weight residual 110.80 118.76 -7.96 2.13e+00 2.20e-01 1.40e+01 angle pdb=" N GLY F 43 " pdb=" CA GLY F 43 " pdb=" C GLY F 43 " ideal model delta sigma weight residual 115.46 109.67 5.79 1.63e+00 3.76e-01 1.26e+01 angle pdb=" CA TYR F 330 " pdb=" CB TYR F 330 " pdb=" CG TYR F 330 " ideal model delta sigma weight residual 113.90 107.51 6.39 1.80e+00 3.09e-01 1.26e+01 ... (remaining 28553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.29: 11771 15.29 - 30.58: 639 30.58 - 45.87: 81 45.87 - 61.17: 3 61.17 - 76.46: 19 Dihedral angle restraints: 12513 sinusoidal: 4972 harmonic: 7541 Sorted by residual: dihedral pdb=" CA GLN A 501 " pdb=" C GLN A 501 " pdb=" N SER A 502 " pdb=" CA SER A 502 " ideal model delta harmonic sigma weight residual -180.00 -149.73 -30.27 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA GLN A1563 " pdb=" C GLN A1563 " pdb=" N TYR A1564 " pdb=" CA TYR A1564 " ideal model delta harmonic sigma weight residual 180.00 149.89 30.11 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA ASN A 308 " pdb=" C ASN A 308 " pdb=" N TYR A 309 " pdb=" CA TYR A 309 " ideal model delta harmonic sigma weight residual -180.00 -150.00 -30.00 0 5.00e+00 4.00e-02 3.60e+01 ... (remaining 12510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2027 0.049 - 0.098: 811 0.098 - 0.147: 241 0.147 - 0.196: 13 0.196 - 0.245: 2 Chirality restraints: 3094 Sorted by residual: chirality pdb=" CA ASN A 998 " pdb=" N ASN A 998 " pdb=" C ASN A 998 " pdb=" CB ASN A 998 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA PRO A2178 " pdb=" N PRO A2178 " pdb=" C PRO A2178 " pdb=" CB PRO A2178 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TYR F 330 " pdb=" N TYR F 330 " pdb=" C TYR F 330 " pdb=" CB TYR F 330 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 3091 not shown) Planarity restraints: 3766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A2250 " 0.048 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO A2251 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A2251 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A2251 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 129 " 0.022 2.00e-02 2.50e+03 1.60e-02 7.05e+00 pdb=" CG TRP B 129 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP B 129 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 129 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 129 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 129 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 129 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 129 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 129 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 129 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP B 129 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A2177 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.50e+00 pdb=" N PRO A2178 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A2178 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A2178 " -0.035 5.00e-02 4.00e+02 ... (remaining 3763 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.53: 223 2.53 - 3.05: 15822 3.05 - 3.56: 22878 3.56 - 4.08: 36865 4.08 - 4.60: 53899 Nonbonded interactions: 129687 Sorted by model distance: nonbonded pdb=" OH TYR B 101 " pdb=" HH TYR B 120 " model vdw 2.010 2.450 nonbonded pdb=" OD1 ASP A2030 " pdb=" OG SER A2181 " model vdw 2.012 2.800 nonbonded pdb=" OG1 THR A1847 " pdb=" OG SER A1881 " model vdw 2.014 2.800 nonbonded pdb=" O GLN A1338 " pdb=" OG SER A1492 " model vdw 2.024 2.800 nonbonded pdb=" O LEU F 146 " pdb=" OG SER F 153 " model vdw 2.043 2.800 ... (remaining 129682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 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: 0.170 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.710 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 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 : 0.009 0.072 20984 Z= 0.403 Angle : 0.921 12.509 28466 Z= 0.502 Chirality : 0.054 0.245 3094 Planarity : 0.006 0.071 3766 Dihedral : 10.079 76.457 7671 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 39.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 21.41 % Favored : 78.43 % Rotamer: Outliers : 0.40 % Allowed : 3.41 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.64 (0.13), residues: 2559 helix: -3.64 (0.20), residues: 251 sheet: -3.59 (0.15), residues: 898 loop : -3.96 (0.14), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 342 TYR 0.039 0.003 TYR A1120 PHE 0.039 0.003 PHE A 656 TRP 0.045 0.004 TRP B 129 HIS 0.009 0.002 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00922 (20984) covalent geometry : angle 0.92098 (28466) hydrogen bonds : bond 0.18063 ( 114) hydrogen bonds : angle 6.17576 ( 291) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 226 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9029 (pp) REVERT: A 749 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7764 (pp) REVERT: A 1768 TYR cc_start: 0.7667 (m-80) cc_final: 0.7299 (m-10) REVERT: A 2209 SER cc_start: 0.9300 (p) cc_final: 0.9025 (m) REVERT: A 2257 PHE cc_start: 0.7735 (t80) cc_final: 0.7469 (t80) REVERT: B 112 ASP cc_start: 0.8183 (t70) cc_final: 0.7932 (t70) REVERT: B 141 GLU cc_start: 0.7544 (tt0) cc_final: 0.7168 (tt0) REVERT: B 142 ILE cc_start: 0.9373 (tt) cc_final: 0.9151 (tt) outliers start: 9 outliers final: 1 residues processed: 234 average time/residue: 0.1714 time to fit residues: 60.8589 Evaluate side-chains 126 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 123 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 962 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 ASN ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1551 GLN ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1742 GLN ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2120 ASN A2236 ASN ** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.063708 restraints weight = 55788.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065101 restraints weight = 31214.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.066509 restraints weight = 23219.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066614 restraints weight = 17429.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.066700 restraints weight = 15905.247| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20984 Z= 0.184 Angle : 0.584 11.858 28466 Z= 0.308 Chirality : 0.043 0.143 3094 Planarity : 0.004 0.049 3766 Dihedral : 6.131 44.863 2842 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 47.74 Ramachandran Plot: Outliers : 0.12 % Allowed : 17.98 % Favored : 81.91 % Rotamer: Outliers : 1.51 % Allowed : 7.09 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.18 (0.14), residues: 2559 helix: -2.92 (0.25), residues: 251 sheet: -3.35 (0.15), residues: 877 loop : -3.68 (0.14), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1196 TYR 0.022 0.002 TYR A1120 PHE 0.019 0.002 PHE A 656 TRP 0.015 0.002 TRP A1996 HIS 0.004 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00416 (20984) covalent geometry : angle 0.58432 (28466) hydrogen bonds : bond 0.03660 ( 114) hydrogen bonds : angle 5.53614 ( 291) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.828 Fit side-chains REVERT: A 678 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9127 (pp) REVERT: A 728 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9015 (pp) REVERT: A 749 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7535 (pp) REVERT: A 1425 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9106 (tm) REVERT: B 112 ASP cc_start: 0.8061 (t70) cc_final: 0.7480 (t0) REVERT: B 142 ILE cc_start: 0.9356 (tt) cc_final: 0.9139 (tt) outliers start: 34 outliers final: 18 residues processed: 161 average time/residue: 0.1413 time to fit residues: 37.5041 Evaluate side-chains 127 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1579 LYS Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2277 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 234 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 190 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1583 ASN ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1818 GLN ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN A2244 ASN ** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.072017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.060059 restraints weight = 57484.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.061451 restraints weight = 32428.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.062497 restraints weight = 23950.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.062610 restraints weight = 18739.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.062699 restraints weight = 17910.259| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 20984 Z= 0.347 Angle : 0.697 9.627 28466 Z= 0.364 Chirality : 0.047 0.170 3094 Planarity : 0.005 0.056 3766 Dihedral : 6.318 47.912 2842 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 48.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 22.31 % Favored : 77.57 % Rotamer: Outliers : 2.35 % Allowed : 8.51 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.16 (0.15), residues: 2559 helix: -2.96 (0.25), residues: 253 sheet: -3.36 (0.16), residues: 908 loop : -3.63 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2273 TYR 0.028 0.002 TYR A1120 PHE 0.035 0.002 PHE A2257 TRP 0.018 0.002 TRP A1996 HIS 0.005 0.002 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00788 (20984) covalent geometry : angle 0.69733 (28466) hydrogen bonds : bond 0.04164 ( 114) hydrogen bonds : angle 5.64526 ( 291) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 109 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 277 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: A 728 ILE cc_start: 0.9373 (OUTLIER) cc_final: 0.9073 (pp) REVERT: A 749 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7418 (pp) REVERT: B 112 ASP cc_start: 0.8125 (t70) cc_final: 0.7858 (t70) REVERT: F 137 GLU cc_start: 0.7781 (tt0) cc_final: 0.7510 (tt0) REVERT: F 365 MET cc_start: 0.8332 (pmm) cc_final: 0.8129 (pmm) outliers start: 53 outliers final: 34 residues processed: 154 average time/residue: 0.1485 time to fit residues: 37.3039 Evaluate side-chains 137 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1314 LEU Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2183 LYS Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2211 THR Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2277 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 124 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 236 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 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 = 0.3264 r_free = 0.3264 target = 0.075328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.063571 restraints weight = 56174.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065210 restraints weight = 30894.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.066287 restraints weight = 21827.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.066360 restraints weight = 17732.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.066508 restraints weight = 16561.949| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20984 Z= 0.102 Angle : 0.511 9.619 28466 Z= 0.266 Chirality : 0.042 0.145 3094 Planarity : 0.003 0.051 3766 Dihedral : 5.539 53.909 2842 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 46.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.79 % Favored : 84.13 % Rotamer: Outliers : 1.77 % Allowed : 9.70 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.71 (0.15), residues: 2559 helix: -2.33 (0.28), residues: 252 sheet: -3.05 (0.17), residues: 878 loop : -3.40 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1484 TYR 0.012 0.001 TYR A1120 PHE 0.022 0.001 PHE A2257 TRP 0.012 0.001 TRP A2180 HIS 0.004 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00226 (20984) covalent geometry : angle 0.51115 (28466) hydrogen bonds : bond 0.02723 ( 114) hydrogen bonds : angle 5.07320 ( 291) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8958 (pp) REVERT: A 749 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7466 (pp) REVERT: B 112 ASP cc_start: 0.8204 (t70) cc_final: 0.7668 (t0) REVERT: F 365 MET cc_start: 0.8337 (pmm) cc_final: 0.8128 (pmm) outliers start: 40 outliers final: 21 residues processed: 153 average time/residue: 0.1492 time to fit residues: 37.5032 Evaluate side-chains 128 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2277 MET Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 6 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1477 ASN A1524 ASN ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN F 333 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.058267 restraints weight = 58309.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.059523 restraints weight = 33244.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.060519 restraints weight = 25240.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.060686 restraints weight = 19786.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.060796 restraints weight = 18648.637| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.066 20984 Z= 0.477 Angle : 0.789 8.028 28466 Z= 0.411 Chirality : 0.050 0.182 3094 Planarity : 0.005 0.063 3766 Dihedral : 6.403 54.333 2842 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 50.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 24.19 % Favored : 75.65 % Rotamer: Outliers : 3.01 % Allowed : 10.63 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.06 (0.15), residues: 2559 helix: -2.82 (0.26), residues: 259 sheet: -3.32 (0.16), residues: 915 loop : -3.55 (0.15), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A2273 TYR 0.029 0.003 TYR A1120 PHE 0.033 0.003 PHE A2257 TRP 0.020 0.003 TRP A1996 HIS 0.006 0.002 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.01084 (20984) covalent geometry : angle 0.78879 (28466) hydrogen bonds : bond 0.04456 ( 114) hydrogen bonds : angle 5.69139 ( 291) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 106 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 277 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7477 (pm20) REVERT: A 728 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.8985 (pp) REVERT: A 749 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7548 (pp) REVERT: A 750 PHE cc_start: 0.7624 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: A 1192 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8837 (mm) REVERT: F 365 MET cc_start: 0.8457 (pmm) cc_final: 0.8057 (pmm) outliers start: 68 outliers final: 42 residues processed: 164 average time/residue: 0.1482 time to fit residues: 39.8872 Evaluate side-chains 149 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 102 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 870 MET Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1315 TYR Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1490 VAL Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain A residue 2183 LYS Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2277 MET Chi-restraints excluded: chain A residue 2370 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 184 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1123 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN A2244 ASN ** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.062657 restraints weight = 56131.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.064619 restraints weight = 31158.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.065870 restraints weight = 19800.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065995 restraints weight = 16419.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066020 restraints weight = 14493.621| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20984 Z= 0.094 Angle : 0.523 8.265 28466 Z= 0.273 Chirality : 0.042 0.169 3094 Planarity : 0.003 0.054 3766 Dihedral : 5.621 57.836 2842 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 47.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.06 % Favored : 83.86 % Rotamer: Outliers : 1.68 % Allowed : 12.41 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.60 (0.15), residues: 2559 helix: -2.24 (0.29), residues: 245 sheet: -3.01 (0.17), residues: 874 loop : -3.30 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1484 TYR 0.014 0.001 TYR F 330 PHE 0.025 0.001 PHE A2257 TRP 0.014 0.001 TRP A2180 HIS 0.004 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00205 (20984) covalent geometry : angle 0.52309 (28466) hydrogen bonds : bond 0.02700 ( 114) hydrogen bonds : angle 5.12968 ( 291) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 749 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7538 (pp) REVERT: B 112 ASP cc_start: 0.8095 (t70) cc_final: 0.7836 (t70) REVERT: F 365 MET cc_start: 0.8390 (pmm) cc_final: 0.8035 (pmm) outliers start: 38 outliers final: 29 residues processed: 143 average time/residue: 0.1442 time to fit residues: 34.1467 Evaluate side-chains 137 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 106 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1315 TYR Chi-restraints excluded: chain A residue 1490 VAL Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2211 THR Chi-restraints excluded: chain A residue 2259 LEU Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 244 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 166 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 9.9990 chunk 169 optimal weight: 0.0050 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN A2244 ASN ** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.060168 restraints weight = 57430.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.061599 restraints weight = 32722.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.062542 restraints weight = 24184.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.062688 restraints weight = 19099.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.062795 restraints weight = 18173.267| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20984 Z= 0.274 Angle : 0.611 8.476 28466 Z= 0.318 Chirality : 0.044 0.157 3094 Planarity : 0.004 0.054 3766 Dihedral : 5.779 58.752 2842 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 46.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 21.53 % Favored : 78.39 % Rotamer: Outliers : 2.17 % Allowed : 12.41 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.65 (0.16), residues: 2559 helix: -2.36 (0.28), residues: 257 sheet: -3.05 (0.17), residues: 912 loop : -3.29 (0.16), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2273 TYR 0.020 0.002 TYR A1120 PHE 0.029 0.002 PHE A2257 TRP 0.016 0.002 TRP A1996 HIS 0.003 0.001 HIS F 344 Details of bonding type rmsd covalent geometry : bond 0.00621 (20984) covalent geometry : angle 0.61137 (28466) hydrogen bonds : bond 0.03365 ( 114) hydrogen bonds : angle 5.22848 ( 291) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 277 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7353 (pm20) REVERT: A 728 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8994 (pp) REVERT: A 749 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.7596 (pp) REVERT: A 750 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: B 112 ASP cc_start: 0.8160 (t70) cc_final: 0.7864 (t70) REVERT: F 137 GLU cc_start: 0.7823 (tt0) cc_final: 0.7551 (tt0) REVERT: F 365 MET cc_start: 0.8461 (pmm) cc_final: 0.8050 (pmm) outliers start: 49 outliers final: 41 residues processed: 145 average time/residue: 0.1429 time to fit residues: 34.4898 Evaluate side-chains 148 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 750 PHE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 870 MET Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1315 TYR Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1490 VAL Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 1875 THR Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2184 TYR Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2211 THR Chi-restraints excluded: chain A residue 2259 LEU Chi-restraints excluded: chain A residue 2370 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 0 optimal weight: 20.0000 chunk 151 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 214 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 190 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.072446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.060581 restraints weight = 57237.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.062045 restraints weight = 32416.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.062926 restraints weight = 24155.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.063078 restraints weight = 19093.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.063224 restraints weight = 18110.263| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20984 Z= 0.234 Angle : 0.588 8.931 28466 Z= 0.307 Chirality : 0.044 0.151 3094 Planarity : 0.004 0.055 3766 Dihedral : 5.717 53.172 2842 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 46.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 19.89 % Favored : 80.03 % Rotamer: Outliers : 2.35 % Allowed : 12.54 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.58 (0.16), residues: 2559 helix: -2.30 (0.29), residues: 257 sheet: -3.00 (0.17), residues: 897 loop : -3.27 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.017 0.001 TYR A1120 PHE 0.032 0.001 PHE A2257 TRP 0.016 0.002 TRP A1996 HIS 0.004 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00531 (20984) covalent geometry : angle 0.58819 (28466) hydrogen bonds : bond 0.03167 ( 114) hydrogen bonds : angle 5.18709 ( 291) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 107 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 277 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: A 728 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9017 (pp) REVERT: A 749 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7614 (pp) REVERT: B 112 ASP cc_start: 0.8168 (t70) cc_final: 0.7860 (t70) REVERT: F 137 GLU cc_start: 0.7833 (tt0) cc_final: 0.7582 (tt0) REVERT: F 365 MET cc_start: 0.8453 (pmm) cc_final: 0.8015 (pmm) outliers start: 53 outliers final: 43 residues processed: 151 average time/residue: 0.1416 time to fit residues: 35.6830 Evaluate side-chains 152 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 106 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1315 TYR Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1490 VAL Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 1875 THR Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2211 THR Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2259 LEU Chi-restraints excluded: chain A residue 2370 ILE Chi-restraints excluded: chain A residue 2396 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 202 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 131 optimal weight: 3.9990 chunk 177 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN A2244 ASN ** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.061296 restraints weight = 56754.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.062756 restraints weight = 32109.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.063700 restraints weight = 23740.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.063871 restraints weight = 18643.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.063975 restraints weight = 17680.351| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20984 Z= 0.186 Angle : 0.548 9.318 28466 Z= 0.285 Chirality : 0.043 0.148 3094 Planarity : 0.003 0.052 3766 Dihedral : 5.487 48.136 2842 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 46.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 19.34 % Favored : 80.58 % Rotamer: Outliers : 2.22 % Allowed : 12.76 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.45 (0.16), residues: 2559 helix: -2.10 (0.30), residues: 251 sheet: -2.96 (0.17), residues: 884 loop : -3.17 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1484 TYR 0.015 0.001 TYR A1120 PHE 0.028 0.001 PHE A2257 TRP 0.015 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00421 (20984) covalent geometry : angle 0.54844 (28466) hydrogen bonds : bond 0.02904 ( 114) hydrogen bonds : angle 5.05089 ( 291) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 112 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.9036 (pp) REVERT: A 749 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7613 (pp) REVERT: B 112 ASP cc_start: 0.8122 (t70) cc_final: 0.7843 (t70) REVERT: F 137 GLU cc_start: 0.7824 (tt0) cc_final: 0.7590 (tt0) REVERT: F 365 MET cc_start: 0.8476 (pmm) cc_final: 0.8045 (pmm) outliers start: 50 outliers final: 42 residues processed: 154 average time/residue: 0.1421 time to fit residues: 36.6069 Evaluate side-chains 153 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 109 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 309 TYR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1315 TYR Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1490 VAL Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 1875 THR Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2211 THR Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2259 LEU Chi-restraints excluded: chain A residue 2370 ILE Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 163 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 141 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 ASN ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2137 GLN ** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.075139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.063448 restraints weight = 56558.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.064954 restraints weight = 31336.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.065766 restraints weight = 23252.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.066051 restraints weight = 18401.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.066183 restraints weight = 17332.716| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20984 Z= 0.100 Angle : 0.493 9.309 28466 Z= 0.255 Chirality : 0.041 0.146 3094 Planarity : 0.003 0.053 3766 Dihedral : 4.994 36.143 2842 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 46.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.01 % Favored : 84.92 % Rotamer: Outliers : 1.42 % Allowed : 13.60 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.20 (0.16), residues: 2559 helix: -1.82 (0.31), residues: 245 sheet: -2.82 (0.17), residues: 889 loop : -2.99 (0.16), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1625 TYR 0.009 0.001 TYR F 292 PHE 0.026 0.001 PHE A2257 TRP 0.012 0.001 TRP A2180 HIS 0.004 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00227 (20984) covalent geometry : angle 0.49335 (28466) hydrogen bonds : bond 0.02445 ( 114) hydrogen bonds : angle 4.76033 ( 291) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5118 Ramachandran restraints generated. 2559 Oldfield, 0 Emsley, 2559 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9036 (pp) REVERT: A 749 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7634 (pp) REVERT: B 112 ASP cc_start: 0.8149 (t70) cc_final: 0.7891 (t70) REVERT: F 137 GLU cc_start: 0.7809 (tt0) cc_final: 0.7598 (tt0) REVERT: F 365 MET cc_start: 0.8462 (pmm) cc_final: 0.8053 (pmm) outliers start: 32 outliers final: 27 residues processed: 149 average time/residue: 0.1463 time to fit residues: 35.9547 Evaluate side-chains 146 residues out of total 2258 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 729 LEU Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 758 MET Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 954 ILE Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1315 TYR Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1490 VAL Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2211 THR Chi-restraints excluded: chain A residue 2259 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 331 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 54 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 233 optimal weight: 1.9990 chunk 1 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 70 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2344 ASN ** 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 = 0.3223 r_free = 0.3223 target = 0.073442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.061620 restraints weight = 56939.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.063262 restraints weight = 31832.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.064008 restraints weight = 23132.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064257 restraints weight = 18563.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.064396 restraints weight = 17638.284| |-----------------------------------------------------------------------------| r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20984 Z= 0.189 Angle : 0.538 9.359 28466 Z= 0.279 Chirality : 0.042 0.148 3094 Planarity : 0.003 0.052 3766 Dihedral : 5.088 36.320 2840 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 45.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 18.41 % Favored : 81.52 % Rotamer: Outliers : 1.77 % Allowed : 13.34 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.23 (0.16), residues: 2559 helix: -1.94 (0.30), residues: 252 sheet: -2.83 (0.17), residues: 892 loop : -3.00 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 342 TYR 0.015 0.001 TYR A1120 PHE 0.031 0.001 PHE A2257 TRP 0.016 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 Details of bonding type rmsd covalent geometry : bond 0.00430 (20984) covalent geometry : angle 0.53811 (28466) hydrogen bonds : bond 0.02872 ( 114) hydrogen bonds : angle 4.83326 ( 291) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2697.17 seconds wall clock time: 48 minutes 30.26 seconds (2910.26 seconds total)