Starting phenix.real_space_refine on Mon Mar 18 09:12:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/03_2024/6h3i_0133.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/03_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_0133/03_2024/6h3i_0133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/03_2024/6h3i_0133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/03_2024/6h3i_0133.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/03_2024/6h3i_0133.pdb" } 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 Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A TYR 717": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 834": "NH1" <-> "NH2" Residue "A TYR 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1311": "NH1" <-> "NH2" Residue "A PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1745": "NH1" <-> "NH2" Residue "A TYR 1766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1988": "NH1" <-> "NH2" Residue "A TYR 2045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2254": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F ARG 40": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 10.26, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.36 Conformation dependent library (CDL) restraints added in 3.5 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: 1.29 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: 4.33 Time building geometry restraints manager: 8.08 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: 97.74 - 105.03: 394 105.03 - 112.31: 10095 112.31 - 119.59: 7042 119.59 - 126.88: 10845 126.88 - 134.16: 182 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 1.850 nonbonded pdb=" OD1 ASP A2030 " pdb=" OG SER A2181 " model vdw 2.012 2.200 nonbonded pdb=" OG1 THR A1847 " pdb=" OG SER A1881 " model vdw 2.014 2.200 nonbonded pdb=" O GLN A1338 " pdb=" OG SER A1492 " model vdw 2.024 2.200 nonbonded pdb=" O LEU F 146 " pdb=" OG SER F 153 " model vdw 2.043 2.200 ... (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 ========== 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: 1.270 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: 0.420 Extract box with map and model: 6.520 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 47.530 Find NCS groups from input model: 0.720 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: 59.770 ------------------------------------------------------------------------------- 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 : 2.183 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: 0.3513 time to fit residues: 124.4006 Evaluate side-chains 125 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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: 6.9990 chunk 195 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 234 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** 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 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 GLN ** A 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 GLN ** 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 ** A2148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2236 ASN ** A2244 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20984 Z= 0.148 Angle : 0.524 11.812 28466 Z= 0.275 Chirality : 0.042 0.142 3094 Planarity : 0.003 0.043 3766 Dihedral : 5.841 45.007 2842 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 51.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.45 % Favored : 83.43 % Rotamer: Outliers : 1.28 % Allowed : 7.04 % Favored : 91.67 % 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: -5.02 (0.15), residues: 2559 helix: -2.70 (0.26), residues: 248 sheet: -3.25 (0.16), residues: 879 loop : -3.58 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.015 0.001 PHE A 656 TYR 0.016 0.001 TYR F 292 ARG 0.003 0.000 ARG A1384 *********************** 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 170 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 2.528 Fit side-chains revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8998 (pp) REVERT: A 749 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7642 (pp) REVERT: A 1425 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9054 (tm) outliers start: 29 outliers final: 18 residues processed: 166 average time/residue: 0.3336 time to fit residues: 90.9397 Evaluate side-chains 128 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 2.474 ------------------------------------------------------------------------------- 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 961 ASP Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1579 LYS 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 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 130 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 chunk 209 optimal weight: 5.9990 chunk 232 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 0.4980 overall best weight: 4.2988 ------------------------------------------------------------------------------- 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 595 GLN ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 20984 Z= 0.365 Angle : 0.612 9.936 28466 Z= 0.318 Chirality : 0.044 0.158 3094 Planarity : 0.004 0.053 3766 Dihedral : 5.853 44.510 2842 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 50.49 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.81 % Favored : 80.07 % Rotamer: Outliers : 2.17 % Allowed : 8.15 % Favored : 89.68 % 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: -4.93 (0.15), residues: 2559 helix: -2.67 (0.26), residues: 260 sheet: -3.22 (0.16), residues: 901 loop : -3.49 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1996 HIS 0.004 0.001 HIS F 344 PHE 0.030 0.002 PHE A2257 TYR 0.026 0.002 TYR A1120 ARG 0.005 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 157 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 108 time to evaluate : 2.231 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8763 (tm) REVERT: A 728 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8937 (pp) REVERT: A 749 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7470 (pp) REVERT: F 137 GLU cc_start: 0.7683 (tt0) cc_final: 0.7440 (tt0) outliers start: 49 outliers final: 32 residues processed: 148 average time/residue: 0.3121 time to fit residues: 75.8338 Evaluate side-chains 135 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 2.431 ------------------------------------------------------------------------------- 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 560 GLN 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 961 ASP 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 1083 ASP 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 1531 ASP Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1765 ASN 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 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 112 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 9.9990 chunk 176 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 112 optimal weight: 0.9990 chunk 157 optimal weight: 0.0970 chunk 235 optimal weight: 9.9990 chunk 249 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 223 optimal weight: 0.0020 chunk 67 optimal weight: 7.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** A1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20984 Z= 0.099 Angle : 0.472 9.246 28466 Z= 0.245 Chirality : 0.041 0.144 3094 Planarity : 0.003 0.047 3766 Dihedral : 5.175 43.268 2842 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 49.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.36 % Favored : 84.56 % Rotamer: Outliers : 1.91 % Allowed : 9.13 % Favored : 88.97 % 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: -4.46 (0.15), residues: 2559 helix: -2.13 (0.29), residues: 253 sheet: -2.90 (0.17), residues: 877 loop : -3.22 (0.15), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.018 0.001 PHE A2257 TYR 0.010 0.001 TYR F 292 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 162 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 119 time to evaluate : 2.257 Fit side-chains revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8937 (pp) REVERT: A 749 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7444 (pp) REVERT: A 1425 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9058 (tm) outliers start: 43 outliers final: 25 residues processed: 153 average time/residue: 0.2988 time to fit residues: 75.2478 Evaluate side-chains 141 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 560 GLN 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 812 PHE Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 962 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1083 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1802 GLU 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 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 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: 5.9990 chunk 185 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 172 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 ASN ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1551 GLN ** 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** A2179 ASN ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 47 GLN F 230 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.054 20984 Z= 0.566 Angle : 0.717 7.787 28466 Z= 0.373 Chirality : 0.047 0.174 3094 Planarity : 0.005 0.055 3766 Dihedral : 6.024 51.205 2842 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 52.75 Ramachandran Plot: Outliers : 0.16 % Allowed : 22.16 % Favored : 77.69 % Rotamer: Outliers : 3.06 % Allowed : 10.15 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.15), residues: 2559 helix: -2.51 (0.27), residues: 261 sheet: -3.06 (0.17), residues: 907 loop : -3.40 (0.15), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1996 HIS 0.006 0.002 HIS F 344 PHE 0.030 0.002 PHE A2257 TYR 0.027 0.002 TYR A1120 ARG 0.007 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 175 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 106 time to evaluate : 2.309 Fit side-chains revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8990 (pp) REVERT: A 749 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7530 (pp) outliers start: 69 outliers final: 46 residues processed: 162 average time/residue: 0.2683 time to fit residues: 72.0887 Evaluate side-chains 149 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 101 time to evaluate : 2.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ASP 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 560 GLN 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 961 ASP 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 1083 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1349 VAL 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 1765 ASN Chi-restraints excluded: chain A residue 1806 ILE Chi-restraints excluded: chain A residue 1874 ASN Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2103 GLU Chi-restraints excluded: chain A residue 2185 ASN 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 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 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: 5.9990 chunk 224 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 0.4980 chunk 61 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 207 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20984 Z= 0.166 Angle : 0.509 7.855 28466 Z= 0.265 Chirality : 0.042 0.148 3094 Planarity : 0.003 0.050 3766 Dihedral : 5.433 58.387 2842 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 50.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.26 % Favored : 83.63 % Rotamer: Outliers : 2.22 % Allowed : 11.43 % 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 (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: -4.37 (0.16), residues: 2559 helix: -1.98 (0.30), residues: 247 sheet: -2.83 (0.17), residues: 877 loop : -3.18 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.026 0.001 PHE A2257 TYR 0.013 0.001 TYR A1120 ARG 0.002 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 164 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 114 time to evaluate : 2.329 Fit side-chains revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9014 (pp) REVERT: A 749 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7517 (pp) REVERT: A 1425 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9185 (tm) REVERT: F 365 MET cc_start: 0.8503 (pmm) cc_final: 0.8005 (pmm) outliers start: 50 outliers final: 38 residues processed: 153 average time/residue: 0.2951 time to fit residues: 74.8149 Evaluate side-chains 149 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 108 time to evaluate : 2.325 ------------------------------------------------------------------------------- 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 560 GLN 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 750 PHE 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 961 ASP 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 1083 ASP Chi-restraints excluded: chain A residue 1243 MET 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 1765 ASN 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 2184 TYR Chi-restraints excluded: chain A residue 2187 LEU Chi-restraints excluded: chain A residue 2211 THR 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 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: 0.8980 chunk 28 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 182 optimal weight: 0.4980 chunk 141 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 248 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 151 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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** A1395 GLN ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8411 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20984 Z= 0.203 Angle : 0.507 8.415 28466 Z= 0.263 Chirality : 0.042 0.144 3094 Planarity : 0.003 0.047 3766 Dihedral : 5.180 58.080 2842 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 49.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 17.98 % Favored : 81.91 % Rotamer: Outliers : 2.30 % Allowed : 11.65 % Favored : 86.04 % 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: -4.21 (0.16), residues: 2559 helix: -1.81 (0.31), residues: 246 sheet: -2.79 (0.17), residues: 887 loop : -3.04 (0.16), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.002 0.001 HIS A1672 PHE 0.022 0.001 PHE A2257 TYR 0.013 0.001 TYR A1120 ARG 0.003 0.000 ARG A2273 *********************** 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 170 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 118 time to evaluate : 2.168 Fit side-chains revert: symmetry clash REVERT: A 560 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7195 (mp10) REVERT: A 728 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.9032 (pp) REVERT: A 749 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7552 (pp) REVERT: F 365 MET cc_start: 0.8515 (pmm) cc_final: 0.8019 (pmm) outliers start: 52 outliers final: 43 residues processed: 160 average time/residue: 0.2922 time to fit residues: 78.0754 Evaluate side-chains 163 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 117 time to evaluate : 2.495 ------------------------------------------------------------------------------- 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 465 GLU Chi-restraints excluded: chain A residue 560 GLN 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 961 ASP 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 1083 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1490 VAL Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1765 ASN 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 2184 TYR Chi-restraints excluded: chain A residue 2185 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 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 94 ASN 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: 7.9990 chunk 99 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 ASN ** A1551 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 20984 Z= 0.469 Angle : 0.644 8.953 28466 Z= 0.335 Chirality : 0.045 0.168 3094 Planarity : 0.004 0.049 3766 Dihedral : 5.685 54.765 2842 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 52.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 21.41 % Favored : 78.47 % Rotamer: Outliers : 2.66 % Allowed : 12.23 % 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 (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: -4.44 (0.16), residues: 2559 helix: -2.12 (0.29), residues: 257 sheet: -2.91 (0.17), residues: 927 loop : -3.17 (0.16), residues: 1375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1996 HIS 0.004 0.001 HIS F 344 PHE 0.029 0.002 PHE A2257 TYR 0.020 0.002 TYR A1120 ARG 0.006 0.001 ARG A 342 *********************** 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 171 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 111 time to evaluate : 2.436 Fit side-chains revert: symmetry clash REVERT: A 728 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9007 (pp) REVERT: A 749 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7555 (pp) REVERT: A 750 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7051 (m-80) REVERT: A 1250 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7509 (tpp) REVERT: F 365 MET cc_start: 0.8526 (pmm) cc_final: 0.8016 (pmm) outliers start: 60 outliers final: 48 residues processed: 157 average time/residue: 0.3022 time to fit residues: 78.3595 Evaluate side-chains 158 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 106 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ASP 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 560 GLN 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 961 ASP 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 1083 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1250 MET Chi-restraints excluded: chain A residue 1349 VAL 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 1638 ASN Chi-restraints excluded: chain A residue 1765 ASN 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 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 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 94 ASN 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: 1.9990 chunk 217 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 100 optimal weight: 0.0570 chunk 181 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 219 optimal weight: 9.9990 chunk 230 optimal weight: 3.9990 chunk 152 optimal weight: 0.8980 overall best weight: 1.9904 ------------------------------------------------------------------------------- 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** A1123 ASN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20984 Z= 0.193 Angle : 0.514 9.229 28466 Z= 0.266 Chirality : 0.042 0.148 3094 Planarity : 0.003 0.049 3766 Dihedral : 5.206 43.236 2842 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 50.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.53 % Favored : 83.35 % Rotamer: Outliers : 2.17 % Allowed : 12.72 % 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 (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: -4.19 (0.16), residues: 2559 helix: -1.81 (0.30), residues: 252 sheet: -2.77 (0.17), residues: 887 loop : -3.02 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.029 0.001 PHE A2257 TYR 0.013 0.001 TYR A1120 ARG 0.004 0.000 ARG A1625 *********************** 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 167 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 118 time to evaluate : 2.216 Fit side-chains revert: symmetry clash REVERT: A 560 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7268 (mp10) REVERT: A 728 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9020 (pp) REVERT: A 749 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7582 (pp) REVERT: A 1192 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8694 (mm) REVERT: A 1250 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.7477 (tpp) REVERT: F 365 MET cc_start: 0.8529 (pmm) cc_final: 0.8084 (pmm) outliers start: 49 outliers final: 42 residues processed: 155 average time/residue: 0.2947 time to fit residues: 76.2216 Evaluate side-chains 160 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 113 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 560 GLN 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 961 ASP 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 1083 ASP Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1250 MET Chi-restraints excluded: chain A residue 1349 VAL Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1765 ASN 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 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 B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 123 ARG 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: 9.9990 chunk 149 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 257 optimal weight: 0.7980 chunk 236 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 21 optimal weight: 0.0670 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 chunk 162 optimal weight: 0.0870 overall best weight: 1.5898 ------------------------------------------------------------------------------- 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** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1524 ASN ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2646 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= 0.162 Angle : 0.480 9.718 28466 Z= 0.247 Chirality : 0.041 0.143 3094 Planarity : 0.003 0.045 3766 Dihedral : 4.730 34.520 2842 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 50.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 16.73 % Favored : 83.20 % Rotamer: Outliers : 2.04 % Allowed : 12.76 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.16), residues: 2559 helix: -1.58 (0.31), residues: 252 sheet: -2.67 (0.17), residues: 894 loop : -2.87 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.026 0.001 PHE A2257 TYR 0.010 0.001 TYR A2341 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 164 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 118 time to evaluate : 2.428 Fit side-chains revert: symmetry clash REVERT: A 560 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7167 (mp10) REVERT: A 728 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9039 (pp) REVERT: A 749 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7551 (pp) REVERT: A 1192 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8593 (mm) REVERT: F 365 MET cc_start: 0.8507 (pmm) cc_final: 0.8004 (pmm) outliers start: 46 outliers final: 36 residues processed: 153 average time/residue: 0.2996 time to fit residues: 76.2061 Evaluate side-chains 153 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 113 time to evaluate : 2.275 ------------------------------------------------------------------------------- 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 560 GLN 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 954 ILE Chi-restraints excluded: chain A residue 961 ASP 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 1083 ASP Chi-restraints excluded: chain A residue 1192 ILE Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1802 GLU Chi-restraints excluded: chain A residue 1874 ASN 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 B residue 53 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 112 ASP Chi-restraints excluded: chain B residue 115 THR 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: 4.9990 chunk 30 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 179 optimal weight: 0.0070 overall best weight: 2.9604 ------------------------------------------------------------------------------- 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** ** A1302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2137 GLN F 333 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062822 restraints weight = 56665.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.064282 restraints weight = 31111.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.064893 restraints weight = 23212.223| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2621 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= 0.252 Angle : 0.521 9.377 28466 Z= 0.270 Chirality : 0.042 0.146 3094 Planarity : 0.003 0.048 3766 Dihedral : 4.884 35.667 2840 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 50.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 17.66 % Favored : 82.26 % Rotamer: Outliers : 2.04 % Allowed : 13.11 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.99 (0.16), residues: 2559 helix: -1.58 (0.31), residues: 252 sheet: -2.65 (0.17), residues: 891 loop : -2.89 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.031 0.001 PHE A2257 TYR 0.014 0.001 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: 3162.36 seconds wall clock time: 61 minutes 10.66 seconds (3670.66 seconds total)