Starting phenix.real_space_refine on Sat Sep 28 22:17:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/09_2024/6h3i_0133.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/09_2024/6h3i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/09_2024/6h3i_0133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/09_2024/6h3i_0133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/09_2024/6h3i_0133.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/09_2024/6h3i_0133.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 11.35, per 1000 atoms: 0.55 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: 4.98 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.61 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: 4.46 Time building geometry restraints manager: 5.91 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: 1.350 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: 0.570 Extract box with map and model: 0.820 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 42.830 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- 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= 0.595 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 : 39.59 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.045 0.004 TRP B 129 HIS 0.009 0.002 HIS A1672 PHE 0.039 0.003 PHE A 656 TYR 0.039 0.003 TYR A1120 ARG 0.010 0.001 ARG A 342 *********************** 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 fitting. rotamer outliers: 9 poor density : 226 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9030 (pp) REVERT: A 749 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7758 (pp) REVERT: A 1768 TYR cc_start: 0.7667 (m-80) cc_final: 0.7300 (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: 0.7492 (t80) REVERT: B 112 ASP cc_start: 0.8183 (t70) cc_final: 0.7937 (t70) REVERT: B 141 GLU cc_start: 0.7544 (tt0) cc_final: 0.7167 (tt0) REVERT: B 142 ILE cc_start: 0.9373 (tt) cc_final: 0.9150 (tt) outliers start: 9 outliers final: 1 residues processed: 234 average time/residue: 0.3739 time to fit residues: 133.1300 Evaluate side-chains 125 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 2.604 ------------------------------------------------------------------------------- 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 217 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 234 optimal weight: 10.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 ** 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 B 47 GLN ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 20984 Z= 0.173 Angle : 0.544 12.036 28466 Z= 0.286 Chirality : 0.042 0.142 3094 Planarity : 0.004 0.045 3766 Dihedral : 5.898 44.208 2842 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 48.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.80 % Favored : 83.12 % Rotamer: Outliers : 1.20 % Allowed : 7.18 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.14), residues: 2559 helix: -2.80 (0.26), residues: 252 sheet: -3.27 (0.15), residues: 882 loop : -3.61 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.014 0.001 PHE A 656 TYR 0.016 0.001 TYR A1120 ARG 0.004 0.000 ARG F 40 *********************** 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 173 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8828 (pp) REVERT: A 749 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7620 (pp) REVERT: A 1425 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9042 (tm) REVERT: B 112 ASP cc_start: 0.7930 (t70) cc_final: 0.7412 (t0) outliers start: 27 outliers final: 15 residues processed: 168 average time/residue: 0.3085 time to fit residues: 83.8425 Evaluate side-chains 128 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 812 PHE Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1409 CYS 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 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 130 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 194 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 234 optimal weight: 20.0000 chunk 253 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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 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** ** 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** ** 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** F 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 20984 Z= 0.434 Angle : 0.658 9.781 28466 Z= 0.344 Chirality : 0.046 0.162 3094 Planarity : 0.004 0.056 3766 Dihedral : 6.117 45.023 2842 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 47.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 20.75 % Favored : 79.13 % Rotamer: Outliers : 1.99 % Allowed : 8.37 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.08 (0.15), residues: 2559 helix: -2.92 (0.25), residues: 264 sheet: -3.30 (0.16), residues: 905 loop : -3.56 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1996 HIS 0.005 0.002 HIS F 344 PHE 0.034 0.002 PHE A2257 TYR 0.028 0.002 TYR A1120 ARG 0.006 0.001 ARG A2273 *********************** 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 156 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 111 time to evaluate : 2.483 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8748 (tm) REVERT: A 728 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8890 (pp) REVERT: A 749 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7481 (pp) REVERT: F 137 GLU cc_start: 0.7710 (tt0) cc_final: 0.7491 (tt0) outliers start: 45 outliers final: 27 residues processed: 148 average time/residue: 0.3231 time to fit residues: 77.4201 Evaluate side-chains 134 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 104 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 LEU 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 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 1349 VAL Chi-restraints excluded: chain A residue 1425 LEU 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 2184 TYR Chi-restraints excluded: chain A residue 2187 LEU 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 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 231 optimal weight: 8.9990 chunk 176 optimal weight: 5.9990 chunk 121 optimal weight: 0.0770 chunk 25 optimal weight: 0.0770 chunk 112 optimal weight: 0.3980 chunk 157 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 249 optimal weight: 9.9990 chunk 123 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 overall best weight: 1.3100 ------------------------------------------------------------------------------- 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 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** ** 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** A2213 ASN A2244 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20984 Z= 0.138 Angle : 0.503 9.253 28466 Z= 0.262 Chirality : 0.042 0.144 3094 Planarity : 0.003 0.049 3766 Dihedral : 5.483 49.358 2842 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 46.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.94 % Favored : 83.98 % Rotamer: Outliers : 1.86 % Allowed : 9.39 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.15), residues: 2559 helix: -2.37 (0.27), residues: 258 sheet: -2.98 (0.17), residues: 861 loop : -3.36 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.021 0.001 PHE A2257 TYR 0.012 0.001 TYR A1120 ARG 0.003 0.000 ARG A1484 *********************** 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 158 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 2.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8913 (pp) REVERT: A 749 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7484 (pp) REVERT: A 1425 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9136 (tm) outliers start: 42 outliers final: 22 residues processed: 149 average time/residue: 0.2977 time to fit residues: 73.9435 Evaluate side-chains 130 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 2.229 ------------------------------------------------------------------------------- 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 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 1425 LEU Chi-restraints excluded: chain A residue 1874 ASN 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 B residue 112 ASP 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 247 LEU Chi-restraints excluded: chain F residue 256 LEU 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 207 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 185 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 212 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 127 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- 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** A1047 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 ASN ** 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** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN A2244 ASN ** A2344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 20984 Z= 0.483 Angle : 0.659 7.602 28466 Z= 0.344 Chirality : 0.046 0.165 3094 Planarity : 0.004 0.054 3766 Dihedral : 5.949 51.797 2842 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 48.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 21.88 % Favored : 77.96 % Rotamer: Outliers : 2.88 % Allowed : 9.84 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.76 (0.15), residues: 2559 helix: -2.54 (0.27), residues: 252 sheet: -3.07 (0.17), residues: 905 loop : -3.39 (0.15), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1996 HIS 0.005 0.001 HIS F 344 PHE 0.028 0.002 PHE A2257 TYR 0.024 0.002 TYR A1120 ARG 0.005 0.001 ARG A2273 *********************** 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 fitting. rotamer outliers: 65 poor density : 109 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8922 (pp) REVERT: A 749 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7553 (pp) REVERT: B 32 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7393 (mm-30) REVERT: F 137 GLU cc_start: 0.7750 (tt0) cc_final: 0.7503 (tt0) outliers start: 65 outliers final: 46 residues processed: 162 average time/residue: 0.2968 time to fit residues: 79.9067 Evaluate side-chains 151 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 103 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 1251 THR Chi-restraints excluded: chain A residue 1315 TYR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1490 VAL 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 1874 ASN Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP 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 2211 THR Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2277 MET Chi-restraints excluded: chain A residue 2370 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 170 ILE 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 130 THR 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 83 optimal weight: 0.0570 chunk 224 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 249 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 0.0040 chunk 131 optimal weight: 0.9980 overall best weight: 1.2114 ------------------------------------------------------------------------------- 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** A1047 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1565 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20984 Z= 0.139 Angle : 0.502 8.010 28466 Z= 0.261 Chirality : 0.041 0.187 3094 Planarity : 0.003 0.049 3766 Dihedral : 5.360 58.585 2842 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 46.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.32 % Favored : 84.60 % Rotamer: Outliers : 1.91 % Allowed : 11.52 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.16), residues: 2559 helix: -2.12 (0.29), residues: 251 sheet: -2.83 (0.17), residues: 867 loop : -3.18 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A2180 HIS 0.004 0.001 HIS A1672 PHE 0.023 0.001 PHE A2257 TYR 0.011 0.001 TYR A1120 ARG 0.003 0.000 ARG A1484 *********************** 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 161 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 118 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8910 (pp) REVERT: A 749 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7520 (pp) REVERT: A 1425 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9141 (tm) REVERT: A 2103 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6955 (pt0) outliers start: 43 outliers final: 31 residues processed: 150 average time/residue: 0.3025 time to fit residues: 74.4278 Evaluate side-chains 150 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU 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 678 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 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 1243 MET Chi-restraints excluded: chain A residue 1315 TYR Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1490 VAL Chi-restraints excluded: chain A residue 1802 GLU Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain A residue 2187 LEU 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 B residue 112 ASP 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 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 240 optimal weight: 10.0000 chunk 28 optimal weight: 0.1980 chunk 142 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 248 optimal weight: 0.0770 chunk 155 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 overall best weight: 3.0544 ------------------------------------------------------------------------------- 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** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20984 Z= 0.259 Angle : 0.527 8.224 28466 Z= 0.274 Chirality : 0.042 0.145 3094 Planarity : 0.003 0.050 3766 Dihedral : 5.324 58.070 2842 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 46.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 18.37 % Favored : 81.56 % Rotamer: Outliers : 2.13 % Allowed : 11.65 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.16), residues: 2559 helix: -2.06 (0.29), residues: 252 sheet: -2.82 (0.17), residues: 878 loop : -3.12 (0.16), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.024 0.001 PHE A2257 TYR 0.014 0.001 TYR A1120 ARG 0.003 0.000 ARG A 342 *********************** 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 163 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 115 time to evaluate : 2.301 Fit side-chains revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8929 (pp) REVERT: A 749 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7567 (pp) REVERT: A 2103 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6924 (pt0) outliers start: 48 outliers final: 38 residues processed: 152 average time/residue: 0.2954 time to fit residues: 74.2650 Evaluate side-chains 154 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 503 LEU 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 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 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 1874 ASN 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 2184 TYR Chi-restraints excluded: chain A residue 2187 LEU 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 B residue 112 ASP 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 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 153 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 195 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20984 Z= 0.146 Angle : 0.492 9.133 28466 Z= 0.255 Chirality : 0.041 0.145 3094 Planarity : 0.003 0.047 3766 Dihedral : 5.034 45.564 2842 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 45.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.71 % Favored : 84.21 % Rotamer: Outliers : 1.86 % Allowed : 12.01 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.16), residues: 2559 helix: -1.86 (0.30), residues: 251 sheet: -2.71 (0.18), residues: 874 loop : -2.99 (0.16), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.019 0.001 PHE A2257 TYR 0.010 0.001 TYR F 330 ARG 0.002 0.000 ARG A1384 *********************** 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 166 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 2.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8944 (pp) REVERT: A 749 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7581 (pp) REVERT: B 32 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7373 (mm-30) outliers start: 42 outliers final: 39 residues processed: 155 average time/residue: 0.2907 time to fit residues: 75.1346 Evaluate side-chains 162 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 121 time to evaluate : 2.286 ------------------------------------------------------------------------------- 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 341 LEU Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 503 LEU 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 823 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 1243 MET Chi-restraints excluded: chain A residue 1315 TYR Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1425 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 2184 TYR Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2259 LEU Chi-restraints excluded: chain A residue 2370 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 ASP 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 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 238 optimal weight: 20.0000 chunk 217 optimal weight: 5.9990 chunk 231 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 219 optimal weight: 8.9990 chunk 230 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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** ** A1025 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** A1395 GLN ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 20984 Z= 0.651 Angle : 0.768 9.864 28466 Z= 0.400 Chirality : 0.049 0.176 3094 Planarity : 0.005 0.066 3766 Dihedral : 6.141 55.243 2842 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 50.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 23.64 % Favored : 76.20 % Rotamer: Outliers : 2.30 % Allowed : 11.96 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.60 (0.16), residues: 2559 helix: -2.36 (0.28), residues: 252 sheet: -3.06 (0.17), residues: 927 loop : -3.20 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1996 HIS 0.007 0.002 HIS A1819 PHE 0.031 0.002 PHE A2257 TYR 0.025 0.002 TYR A1120 ARG 0.008 0.001 ARG A1237 *********************** 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 161 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 109 time to evaluate : 2.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8903 (pp) REVERT: A 749 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7567 (pp) REVERT: A 750 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.7065 (m-80) REVERT: A 2103 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.7153 (pt0) REVERT: B 32 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7357 (mm-30) outliers start: 52 outliers final: 39 residues processed: 150 average time/residue: 0.3615 time to fit residues: 90.4632 Evaluate side-chains 149 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 106 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 503 LEU 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 750 PHE Chi-restraints excluded: chain A residue 812 PHE Chi-restraints excluded: chain A residue 823 ILE 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 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 1425 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 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2103 GLU 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 B residue 62 SER Chi-restraints excluded: chain B residue 112 ASP 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 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 245 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 257 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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** ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 0.035 20984 Z= 0.231 Angle : 0.553 9.267 28466 Z= 0.288 Chirality : 0.043 0.148 3094 Planarity : 0.003 0.050 3766 Dihedral : 5.566 44.997 2842 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 47.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 17.35 % Favored : 82.57 % Rotamer: Outliers : 1.82 % Allowed : 12.63 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.16), residues: 2559 helix: -2.10 (0.29), residues: 251 sheet: -2.79 (0.18), residues: 865 loop : -3.13 (0.16), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1996 HIS 0.005 0.001 HIS A1672 PHE 0.031 0.001 PHE A2257 TYR 0.016 0.001 TYR A1120 ARG 0.003 0.000 ARG A1484 ********************** 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 154 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8921 (pp) REVERT: A 749 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7563 (pp) REVERT: A 1192 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8720 (mm) REVERT: B 32 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7342 (mm-30) outliers start: 41 outliers final: 36 residues processed: 145 average time/residue: 0.3022 time to fit residues: 73.3887 Evaluate side-chains 149 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 110 time to evaluate : 2.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 503 LEU 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 812 PHE Chi-restraints excluded: chain A residue 823 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 1315 TYR Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1490 VAL Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1857 THR Chi-restraints excluded: chain A residue 1874 ASN 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 2259 LEU Chi-restraints excluded: chain A residue 2370 ILE Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 112 ASP 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 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 218 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 chunk 188 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 210 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.060494 restraints weight = 57170.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.061856 restraints weight = 32818.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.062886 restraints weight = 24237.339| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20984 Z= 0.368 Angle : 0.596 8.973 28466 Z= 0.310 Chirality : 0.044 0.153 3094 Planarity : 0.004 0.050 3766 Dihedral : 5.624 45.926 2842 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 47.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 21.02 % Favored : 78.94 % Rotamer: Outliers : 1.91 % Allowed : 12.45 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.39 (0.16), residues: 2559 helix: -2.20 (0.29), residues: 257 sheet: -2.83 (0.17), residues: 890 loop : -3.15 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.033 0.002 PHE A2257 TYR 0.019 0.002 TYR A1120 ARG 0.004 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3225.20 seconds wall clock time: 60 minutes 3.52 seconds (3603.52 seconds total)