Starting phenix.real_space_refine (version: dev) on Wed Apr 6 12:01:37 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/04_2022/6h3i_0133.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/04_2022/6h3i_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_0133/04_2022/6h3i_0133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/04_2022/6h3i_0133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/04_2022/6h3i_0133.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3i_0133/04_2022/6h3i_0133.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4553/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: 12.91, per 1000 atoms: 0.63 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: 9.05 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: 0.44 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: 4.23 Time building geometry restraints manager: 9.75 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 0.530 Extract box with map and model: 7.420 Check model and map are aligned: 0.340 Convert atoms to be neutral: 0.190 Process input model: 53.270 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 % 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 *********************** 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 : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 234 average time/residue: 0.3589 time to fit residues: 128.6004 Evaluate side-chains 121 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 2.538 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1855 time to fit residues: 3.7483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 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: 5.9990 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 ** 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** ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.087 20984 Z= 0.165 Angle : 0.535 11.852 28466 Z= 0.280 Chirality : 0.042 0.142 3094 Planarity : 0.004 0.073 3766 Dihedral : 5.651 25.990 2836 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 51.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.26 % Favored : 83.63 % Rotamer Outliers : 1.28 % 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: -5.01 (0.15), residues: 2559 helix: -2.69 (0.26), residues: 248 sheet: -3.24 (0.16), residues: 879 loop : -3.58 (0.15), residues: 1432 *********************** 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: 29 poor density : 144 time to evaluate : 2.563 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 19 residues processed: 168 average time/residue: 0.3119 time to fit residues: 84.8293 Evaluate side-chains 124 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 2.632 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2061 time to fit residues: 10.2190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 234 optimal weight: 5.9990 chunk 253 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 232 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 188 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- 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 A 727 GLN A 734 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 20984 Z= 0.386 Angle : 0.630 13.089 28466 Z= 0.327 Chirality : 0.044 0.158 3094 Planarity : 0.005 0.124 3766 Dihedral : 5.687 27.459 2836 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 50.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.77 % Favored : 80.11 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.95 (0.15), residues: 2559 helix: -2.67 (0.26), residues: 260 sheet: -3.15 (0.16), residues: 866 loop : -3.58 (0.15), residues: 1433 *********************** 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 142 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 2.658 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 17 residues processed: 137 average time/residue: 0.3132 time to fit residues: 70.9980 Evaluate side-chains 117 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 100 time to evaluate : 2.629 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2023 time to fit residues: 9.9119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 10.0000 chunk 176 optimal weight: 9.9990 chunk 121 optimal weight: 0.0000 chunk 25 optimal weight: 0.8980 chunk 112 optimal weight: 0.0980 chunk 157 optimal weight: 2.9990 chunk 235 optimal weight: 20.0000 chunk 249 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 223 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** ** 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** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.098 20984 Z= 0.212 Angle : 0.531 12.774 28466 Z= 0.276 Chirality : 0.042 0.144 3094 Planarity : 0.004 0.094 3766 Dihedral : 5.263 25.128 2836 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 49.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.41 % Favored : 83.47 % Rotamer Outliers : 1.20 % 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: -4.62 (0.15), residues: 2559 helix: -2.27 (0.28), residues: 254 sheet: -2.97 (0.17), residues: 856 loop : -3.37 (0.15), residues: 1449 *********************** 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 135 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 108 time to evaluate : 2.538 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 126 average time/residue: 0.3266 time to fit residues: 68.9821 Evaluate side-chains 115 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 2.382 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2105 time to fit residues: 8.5318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 212 optimal weight: 20.0000 chunk 172 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 127 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 GLN ** 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** A1583 ASN ** 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** B 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.068 20984 Z= 0.429 Angle : 0.639 14.604 28466 Z= 0.333 Chirality : 0.045 0.160 3094 Planarity : 0.004 0.088 3766 Dihedral : 5.575 27.496 2836 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 51.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 21.22 % Favored : 78.66 % Rotamer Outliers : 1.60 % 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: -4.69 (0.15), residues: 2559 helix: -2.41 (0.27), residues: 259 sheet: -3.00 (0.17), residues: 891 loop : -3.39 (0.15), residues: 1409 *********************** 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 144 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 108 time to evaluate : 2.818 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 15 residues processed: 129 average time/residue: 0.3131 time to fit residues: 67.2826 Evaluate side-chains 115 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 2.613 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2168 time to fit residues: 9.4599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 249 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 115 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- 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 238 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** 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** ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.122 20984 Z= 0.240 Angle : 0.552 15.130 28466 Z= 0.287 Chirality : 0.042 0.168 3094 Planarity : 0.003 0.079 3766 Dihedral : 5.252 25.355 2836 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 50.52 Ramachandran Plot: Outliers : 0.12 % Allowed : 16.84 % Favored : 83.04 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.45 (0.16), residues: 2559 helix: -2.08 (0.29), residues: 254 sheet: -2.87 (0.17), residues: 865 loop : -3.26 (0.15), residues: 1440 *********************** 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 133 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 2.523 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 128 average time/residue: 0.3205 time to fit residues: 67.7694 Evaluate side-chains 116 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 103 time to evaluate : 2.749 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2037 time to fit residues: 8.5780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 155 optimal weight: 8.9990 chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 ASN ** A1190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 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** ** 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: 0.8644 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.201 20984 Z= 0.321 Angle : 0.582 19.288 28466 Z= 0.305 Chirality : 0.043 0.146 3094 Planarity : 0.004 0.111 3766 Dihedral : 5.217 26.393 2836 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 50.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.58 % Favored : 80.30 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.16), residues: 2559 helix: -1.96 (0.30), residues: 246 sheet: -2.83 (0.18), residues: 866 loop : -3.20 (0.15), residues: 1447 *********************** 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 130 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 2.449 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 124 average time/residue: 0.3261 time to fit residues: 66.8517 Evaluate side-chains 117 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 105 time to evaluate : 2.694 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2252 time to fit residues: 8.4062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.337 20984 Z= 0.396 Angle : 0.621 28.193 28466 Z= 0.331 Chirality : 0.043 0.147 3094 Planarity : 0.004 0.091 3766 Dihedral : 5.328 26.008 2836 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 50.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.38 % Favored : 80.50 % Rotamer Outliers : 0.62 % 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: -2.10 (0.29), residues: 257 sheet: -2.81 (0.18), residues: 860 loop : -3.19 (0.15), residues: 1442 *********************** 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 121 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 2.597 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 115 average time/residue: 0.3445 time to fit residues: 65.0732 Evaluate side-chains 110 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2340 time to fit residues: 7.1927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 231 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 181 optimal weight: 9.9990 chunk 71 optimal weight: 8.9990 chunk 209 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 230 optimal weight: 10.0000 chunk 152 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1123 ASN ** A1302 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** ** 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** F 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 20984 Z= 0.405 Angle : 0.633 14.921 28466 Z= 0.328 Chirality : 0.044 0.154 3094 Planarity : 0.004 0.078 3766 Dihedral : 5.487 27.404 2836 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 51.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 21.26 % Favored : 78.62 % Rotamer Outliers : 0.31 % 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: -4.45 (0.16), residues: 2559 helix: -2.16 (0.29), residues: 257 sheet: -2.86 (0.17), residues: 891 loop : -3.23 (0.16), residues: 1411 *********************** 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 113 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 2.728 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 111 average time/residue: 0.3290 time to fit residues: 60.5531 Evaluate side-chains 107 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 2.424 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2398 time to fit residues: 5.8699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 0.0870 chunk 149 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 170 optimal weight: 0.8980 chunk 257 optimal weight: 6.9990 chunk 236 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 158 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.3362 ------------------------------------------------------------------------------- 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 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** ** 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** A2248 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.151 20984 Z= 0.730 Angle : 0.887 106.058 28466 Z= 0.388 Chirality : 0.043 0.161 3094 Planarity : 0.004 0.079 3766 Dihedral : 5.456 27.017 2836 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 52.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 21.14 % Favored : 78.74 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.04 % 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: -4.42 (0.16), residues: 2559 helix: -2.09 (0.29), residues: 251 sheet: -2.86 (0.17), residues: 877 loop : -3.21 (0.16), residues: 1431 ********************** 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 108 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 2.614 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 105 average time/residue: 0.3306 time to fit residues: 57.2405 Evaluate side-chains 106 residues out of total 2258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 2.630 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1870 time to fit residues: 4.8664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 188 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 205 optimal weight: 9.9990 chunk 85 optimal weight: 8.9990 chunk 210 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1302 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.062223 restraints weight = 56051.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.063636 restraints weight = 31384.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064617 restraints weight = 23553.756| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.151 20984 Z= 0.730 Angle : 0.887 106.057 28466 Z= 0.388 Chirality : 0.043 0.161 3094 Planarity : 0.004 0.079 3766 Dihedral : 5.456 27.017 2836 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 52.80 Ramachandran Plot: Outliers : 0.12 % Allowed : 21.14 % Favored : 78.74 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.04 % 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: -4.42 (0.16), residues: 2559 helix: -2.09 (0.29), residues: 251 sheet: -2.86 (0.17), residues: 877 loop : -3.21 (0.16), residues: 1431 =============================================================================== Job complete usr+sys time: 3000.04 seconds wall clock time: 57 minutes 15.62 seconds (3435.62 seconds total)