Starting phenix.real_space_refine on Thu Mar 14 13:19:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/03_2024/7zk9_14759_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/03_2024/7zk9_14759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/03_2024/7zk9_14759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/03_2024/7zk9_14759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/03_2024/7zk9_14759_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/03_2024/7zk9_14759_updated.pdb" } resolution = 4.3 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= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5781 2.51 5 N 1533 2.21 5 O 1651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 251": "OE1" <-> "OE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 912": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 968": "OE1" <-> "OE2" Residue "A GLU 1080": "OE1" <-> "OE2" Residue "A GLU 1205": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8999 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1158, 8999 Unusual residues: {'JIZ': 1} Inner-chain residues flagged as termini: ['pdbres="LYS A1260 "'] Classifications: {'peptide': 1157, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 1127, None: 1} Not linked: pdbres="LYS A1260 " pdbres="JIZ A1301 " Chain breaks: 1 Time building chain proxies: 4.54, per 1000 atoms: 0.50 Number of scatterers: 8999 At special positions: 0 Unit cell: (76.167, 112.158, 146.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1651 8.00 N 1533 7.00 C 5781 6.00 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: 3.90 Conformation dependent library (CDL) restraints added in 1.8 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 3 sheets defined 61.3% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 44 through 81 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 87 through 153 removed outlier: 4.458A pdb=" N MET A 91 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA A 94 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N MET A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 145 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 165 through 206 removed outlier: 5.834A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLY A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 255 Proline residue: A 219 - end of helix removed outlier: 4.206A pdb=" N LYS A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 271 through 318 Processing helix chain 'A' and resid 324 through 364 removed outlier: 3.700A pdb=" N SER A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix removed outlier: 3.786A pdb=" N GLY A 356 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 493 through 499 Processing helix chain 'A' and resid 529 through 543 Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.029A pdb=" N GLY A 575 " --> pdb=" O LYS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 Processing helix chain 'A' and resid 696 through 699 No H-bonds generated for 'chain 'A' and resid 696 through 699' Processing helix chain 'A' and resid 704 through 735 removed outlier: 3.809A pdb=" N VAL A 709 " --> pdb=" O PRO A 705 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N GLY A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 711 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 3.710A pdb=" N PHE A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 794 removed outlier: 4.057A pdb=" N LYS A 775 " --> pdb=" O PHE A 771 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS A 790 " --> pdb=" O TYR A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 801 Processing helix chain 'A' and resid 807 through 816 Processing helix chain 'A' and resid 819 through 849 removed outlier: 3.625A pdb=" N GLY A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER A 827 " --> pdb=" O GLY A 823 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ARG A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 829 " --> pdb=" O THR A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 885 Proline residue: A 862 - end of helix Processing helix chain 'A' and resid 887 through 898 Processing helix chain 'A' and resid 900 through 905 Processing helix chain 'A' and resid 910 through 961 Proline residue: A 923 - end of helix removed outlier: 3.732A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 990 Processing helix chain 'A' and resid 998 through 1009 Processing helix chain 'A' and resid 1069 through 1079 removed outlier: 3.607A pdb=" N THR A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N VAL A1075 " --> pdb=" O GLY A1071 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1076 " --> pdb=" O LYS A1072 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A1079 " --> pdb=" O VAL A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1108 Processing helix chain 'A' and resid 1123 through 1131 removed outlier: 3.737A pdb=" N TYR A1129 " --> pdb=" O GLU A1125 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY A1130 " --> pdb=" O ASN A1126 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASP A1131 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 Processing helix chain 'A' and resid 1151 through 1156 Processing helix chain 'A' and resid 1160 through 1162 No H-bonds generated for 'chain 'A' and resid 1160 through 1162' Processing helix chain 'A' and resid 1174 through 1188 removed outlier: 4.621A pdb=" N GLN A1178 " --> pdb=" O GLY A1174 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A1179 " --> pdb=" O GLY A1175 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1220 Processing helix chain 'A' and resid 1230 through 1235 Processing helix chain 'A' and resid 1251 through 1254 No H-bonds generated for 'chain 'A' and resid 1251 through 1254' Processing sheet with id= A, first strand: chain 'A' and resid 389 through 391 Processing sheet with id= B, first strand: chain 'A' and resid 419 through 421 Processing sheet with id= C, first strand: chain 'A' and resid 1061 through 1064 removed outlier: 7.311A pdb=" N VAL A1223 " --> pdb=" O LEU A1062 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LEU A1064 " --> pdb=" O VAL A1223 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL A1225 " --> pdb=" O LEU A1064 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N ILE A1226 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY A1110 " --> pdb=" O LEU A1194 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 520 hydrogen bonds defined for protein. 1551 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1478 1.31 - 1.44: 2369 1.44 - 1.56: 5251 1.56 - 1.69: 8 1.69 - 1.82: 60 Bond restraints: 9166 Sorted by residual: bond pdb=" C03 JIZ A1301 " pdb=" N02 JIZ A1301 " ideal model delta sigma weight residual 1.367 1.638 -0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C08 JIZ A1301 " pdb=" N04 JIZ A1301 " ideal model delta sigma weight residual 1.366 1.615 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C13 JIZ A1301 " pdb=" N06 JIZ A1301 " ideal model delta sigma weight residual 1.366 1.613 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C02 JIZ A1301 " pdb=" S01 JIZ A1301 " ideal model delta sigma weight residual 1.728 1.547 0.181 2.00e-02 2.50e+03 8.16e+01 bond pdb=" C03 JIZ A1301 " pdb=" C04 JIZ A1301 " ideal model delta sigma weight residual 1.360 1.519 -0.159 2.00e-02 2.50e+03 6.30e+01 ... (remaining 9161 not shown) Histogram of bond angle deviations from ideal: 97.82 - 105.11: 121 105.11 - 112.40: 4609 112.40 - 119.69: 3362 119.69 - 126.98: 4228 126.98 - 134.26: 73 Bond angle restraints: 12393 Sorted by residual: angle pdb=" N SER A1206 " pdb=" CA SER A1206 " pdb=" C SER A1206 " ideal model delta sigma weight residual 112.54 105.29 7.25 1.22e+00 6.72e-01 3.53e+01 angle pdb=" C07 JIZ A1301 " pdb=" S02 JIZ A1301 " pdb=" C09 JIZ A1301 " ideal model delta sigma weight residual 89.67 107.35 -17.68 3.00e+00 1.11e-01 3.47e+01 angle pdb=" C12 JIZ A1301 " pdb=" S03 JIZ A1301 " pdb=" C14 JIZ A1301 " ideal model delta sigma weight residual 89.68 107.08 -17.40 3.00e+00 1.11e-01 3.37e+01 angle pdb=" N PHE A1082 " pdb=" CA PHE A1082 " pdb=" C PHE A1082 " ideal model delta sigma weight residual 111.28 105.53 5.75 1.09e+00 8.42e-01 2.78e+01 angle pdb=" C02 JIZ A1301 " pdb=" S01 JIZ A1301 " pdb=" C04 JIZ A1301 " ideal model delta sigma weight residual 89.57 105.17 -15.60 3.00e+00 1.11e-01 2.70e+01 ... (remaining 12388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4963 17.61 - 35.22: 413 35.22 - 52.82: 83 52.82 - 70.43: 9 70.43 - 88.04: 8 Dihedral angle restraints: 5476 sinusoidal: 2165 harmonic: 3311 Sorted by residual: dihedral pdb=" CA PHE A 707 " pdb=" C PHE A 707 " pdb=" N VAL A 708 " pdb=" CA VAL A 708 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA MET A 99 " pdb=" C MET A 99 " pdb=" N PHE A 100 " pdb=" CA PHE A 100 " ideal model delta harmonic sigma weight residual 180.00 160.85 19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA PRO A 740 " pdb=" C PRO A 740 " pdb=" N PRO A 741 " pdb=" CA PRO A 741 " ideal model delta harmonic sigma weight residual 180.00 -160.90 -19.10 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 5473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1071 0.058 - 0.116: 248 0.116 - 0.174: 62 0.174 - 0.232: 33 0.232 - 0.290: 9 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CA VAL A1075 " pdb=" N VAL A1075 " pdb=" C VAL A1075 " pdb=" CB VAL A1075 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA LEU A 519 " pdb=" N LEU A 519 " pdb=" C LEU A 519 " pdb=" CB LEU A 519 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA TYR A1083 " pdb=" N TYR A1083 " pdb=" C TYR A1083 " pdb=" CB TYR A1083 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1420 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 964 " -0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C LEU A 964 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A 964 " -0.022 2.00e-02 2.50e+03 pdb=" N MET A 965 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 205 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.38e+00 pdb=" C THR A 205 " 0.050 2.00e-02 2.50e+03 pdb=" O THR A 205 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG A 206 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 507 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.63e+00 pdb=" C ASP A 507 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 507 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 508 " -0.015 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2004 2.78 - 3.31: 10029 3.31 - 3.84: 15092 3.84 - 4.37: 17094 4.37 - 4.90: 27425 Nonbonded interactions: 71644 Sorted by model distance: nonbonded pdb=" O ASN A1149 " pdb=" NH2 ARG A1179 " model vdw 2.255 2.520 nonbonded pdb=" O ALA A 192 " pdb=" OG SER A 340 " model vdw 2.267 2.440 nonbonded pdb=" O ALA A 288 " pdb=" ND2 ASN A 292 " model vdw 2.284 2.520 nonbonded pdb=" O LEU A 316 " pdb=" OG SER A 319 " model vdw 2.294 2.440 nonbonded pdb=" O ALA A 256 " pdb=" OG1 THR A 259 " model vdw 2.301 2.440 ... (remaining 71639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.170 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.150 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 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 0.271 9166 Z= 0.620 Angle : 1.002 17.683 12393 Z= 0.660 Chirality : 0.063 0.290 1423 Planarity : 0.004 0.039 1578 Dihedral : 13.586 88.038 3354 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 0.74 % Allowed : 2.01 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1153 helix: 1.04 (0.19), residues: 732 sheet: -1.02 (0.70), residues: 49 loop : -2.09 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 704 HIS 0.002 0.000 HIS A1151 PHE 0.019 0.002 PHE A 100 TYR 0.022 0.001 TYR A 924 ARG 0.009 0.001 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 273 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9265 (mt) cc_final: 0.8921 (tp) REVERT: A 75 THR cc_start: 0.9537 (p) cc_final: 0.9333 (p) REVERT: A 76 ASP cc_start: 0.8951 (m-30) cc_final: 0.8525 (m-30) REVERT: A 100 PHE cc_start: 0.8316 (m-10) cc_final: 0.8052 (m-10) REVERT: A 103 LEU cc_start: 0.9472 (tp) cc_final: 0.9147 (tp) REVERT: A 160 ASP cc_start: 0.8800 (m-30) cc_final: 0.8469 (m-30) REVERT: A 188 MET cc_start: 0.8620 (tpp) cc_final: 0.8256 (mmm) REVERT: A 191 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8921 (tm-30) REVERT: A 209 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8338 (mptt) REVERT: A 295 MET cc_start: 0.8575 (ttm) cc_final: 0.8356 (ttm) REVERT: A 471 GLN cc_start: 0.8887 (pt0) cc_final: 0.8548 (pt0) REVERT: A 754 LEU cc_start: 0.9044 (mt) cc_final: 0.8791 (mt) REVERT: A 787 MET cc_start: 0.7680 (mmt) cc_final: 0.7270 (mtt) REVERT: A 828 ARG cc_start: 0.9099 (tpt170) cc_final: 0.8713 (tpt90) REVERT: A 872 MET cc_start: 0.7337 (mmp) cc_final: 0.7112 (mmm) REVERT: A 928 MET cc_start: 0.9013 (mpp) cc_final: 0.8752 (mpp) REVERT: A 953 PHE cc_start: 0.8634 (m-80) cc_final: 0.8315 (m-80) REVERT: A 955 PHE cc_start: 0.8848 (t80) cc_final: 0.8087 (t80) REVERT: A 960 VAL cc_start: 0.9389 (t) cc_final: 0.9158 (t) REVERT: A 1162 ASN cc_start: 0.9106 (t0) cc_final: 0.8852 (t0) outliers start: 7 outliers final: 2 residues processed: 278 average time/residue: 0.1767 time to fit residues: 71.0544 Evaluate side-chains 230 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 227 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 ASN A 969 ASN A1253 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9166 Z= 0.212 Angle : 0.573 9.583 12393 Z= 0.314 Chirality : 0.041 0.158 1423 Planarity : 0.004 0.045 1578 Dihedral : 4.868 40.764 1274 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.24), residues: 1153 helix: 1.17 (0.19), residues: 740 sheet: -0.86 (0.71), residues: 49 loop : -2.14 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 704 HIS 0.004 0.001 HIS A 60 PHE 0.021 0.002 PHE A 131 TYR 0.022 0.001 TYR A 924 ARG 0.004 0.000 ARG A 828 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ILE cc_start: 0.9444 (mt) cc_final: 0.9174 (tp) REVERT: A 75 THR cc_start: 0.9560 (p) cc_final: 0.9323 (p) REVERT: A 76 ASP cc_start: 0.9059 (m-30) cc_final: 0.8595 (m-30) REVERT: A 99 MET cc_start: 0.8472 (pmm) cc_final: 0.8231 (pmm) REVERT: A 100 PHE cc_start: 0.8234 (m-10) cc_final: 0.7948 (m-10) REVERT: A 103 LEU cc_start: 0.9534 (tp) cc_final: 0.9177 (tp) REVERT: A 107 MET cc_start: 0.9432 (mmp) cc_final: 0.9219 (mmp) REVERT: A 160 ASP cc_start: 0.8696 (m-30) cc_final: 0.8333 (m-30) REVERT: A 191 GLN cc_start: 0.9337 (tm-30) cc_final: 0.9068 (tm-30) REVERT: A 195 THR cc_start: 0.8649 (m) cc_final: 0.8357 (m) REVERT: A 209 LYS cc_start: 0.9040 (ptpp) cc_final: 0.8794 (mptt) REVERT: A 438 ARG cc_start: 0.8568 (mtt180) cc_final: 0.8339 (mtt180) REVERT: A 749 ASN cc_start: 0.8882 (m-40) cc_final: 0.8507 (m-40) REVERT: A 754 LEU cc_start: 0.9130 (mt) cc_final: 0.8856 (mt) REVERT: A 787 MET cc_start: 0.7899 (mmt) cc_final: 0.7599 (mtt) REVERT: A 872 MET cc_start: 0.7399 (mmp) cc_final: 0.7123 (mmm) REVERT: A 882 ASP cc_start: 0.8301 (m-30) cc_final: 0.7836 (m-30) REVERT: A 928 MET cc_start: 0.9098 (mpp) cc_final: 0.8882 (mpp) REVERT: A 930 LYS cc_start: 0.8779 (ttpt) cc_final: 0.7882 (ptpp) REVERT: A 938 PHE cc_start: 0.9424 (t80) cc_final: 0.9192 (t80) REVERT: A 953 PHE cc_start: 0.8630 (m-80) cc_final: 0.8370 (m-80) REVERT: A 955 PHE cc_start: 0.8788 (t80) cc_final: 0.8036 (t80) REVERT: A 960 VAL cc_start: 0.9452 (t) cc_final: 0.9223 (t) REVERT: A 1080 GLU cc_start: 0.8124 (pm20) cc_final: 0.7374 (pm20) REVERT: A 1134 ARG cc_start: 0.8500 (mtp-110) cc_final: 0.7977 (mtm180) REVERT: A 1205 GLU cc_start: 0.9001 (tt0) cc_final: 0.8715 (tp30) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.1775 time to fit residues: 66.9682 Evaluate side-chains 225 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 83 optimal weight: 0.9980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 83 GLN ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9166 Z= 0.259 Angle : 0.589 10.277 12393 Z= 0.327 Chirality : 0.041 0.150 1423 Planarity : 0.004 0.039 1578 Dihedral : 4.892 42.721 1274 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.21 % Allowed : 4.12 % Favored : 95.67 % 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: -0.08 (0.24), residues: 1153 helix: 0.98 (0.19), residues: 742 sheet: -0.81 (0.72), residues: 49 loop : -2.12 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 704 HIS 0.006 0.001 HIS A 60 PHE 0.071 0.002 PHE A 934 TYR 0.022 0.002 TYR A 924 ARG 0.002 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 253 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9057 (pmm) cc_final: 0.8688 (pmm) REVERT: A 58 ILE cc_start: 0.9516 (mt) cc_final: 0.9240 (tp) REVERT: A 100 PHE cc_start: 0.8246 (m-10) cc_final: 0.7896 (m-10) REVERT: A 103 LEU cc_start: 0.9568 (tp) cc_final: 0.9252 (tp) REVERT: A 191 GLN cc_start: 0.9393 (tm-30) cc_final: 0.9016 (tm-30) REVERT: A 209 LYS cc_start: 0.9056 (ptpp) cc_final: 0.8818 (mptt) REVERT: A 237 ASP cc_start: 0.8596 (m-30) cc_final: 0.8108 (p0) REVERT: A 359 TYR cc_start: 0.8887 (t80) cc_final: 0.8051 (t80) REVERT: A 406 LEU cc_start: 0.8975 (mm) cc_final: 0.8765 (mm) REVERT: A 438 ARG cc_start: 0.8646 (mtt180) cc_final: 0.8262 (mtt180) REVERT: A 558 ASP cc_start: 0.8663 (m-30) cc_final: 0.8427 (t0) REVERT: A 749 ASN cc_start: 0.8924 (m-40) cc_final: 0.8551 (m-40) REVERT: A 754 LEU cc_start: 0.9158 (mt) cc_final: 0.8904 (mt) REVERT: A 787 MET cc_start: 0.7938 (mmt) cc_final: 0.7627 (mtt) REVERT: A 872 MET cc_start: 0.7391 (mmp) cc_final: 0.7030 (mmm) REVERT: A 897 ILE cc_start: 0.9484 (mt) cc_final: 0.9035 (tp) REVERT: A 928 MET cc_start: 0.9081 (mpp) cc_final: 0.8847 (mpp) REVERT: A 934 PHE cc_start: 0.8687 (m-80) cc_final: 0.8482 (m-80) REVERT: A 938 PHE cc_start: 0.9394 (t80) cc_final: 0.9153 (t80) REVERT: A 953 PHE cc_start: 0.8576 (m-80) cc_final: 0.8328 (m-80) REVERT: A 955 PHE cc_start: 0.8796 (t80) cc_final: 0.8013 (t80) REVERT: A 960 VAL cc_start: 0.9481 (t) cc_final: 0.9266 (t) REVERT: A 1134 ARG cc_start: 0.8562 (mtp-110) cc_final: 0.8199 (mtp180) outliers start: 2 outliers final: 0 residues processed: 254 average time/residue: 0.1835 time to fit residues: 67.3667 Evaluate side-chains 225 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 99 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN A 969 ASN ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9166 Z= 0.264 Angle : 0.588 9.551 12393 Z= 0.327 Chirality : 0.041 0.183 1423 Planarity : 0.004 0.042 1578 Dihedral : 4.980 42.587 1274 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.11 % Allowed : 4.65 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.24), residues: 1153 helix: 0.87 (0.19), residues: 740 sheet: -0.74 (0.74), residues: 49 loop : -2.16 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 694 HIS 0.006 0.001 HIS A 60 PHE 0.036 0.002 PHE A 204 TYR 0.021 0.002 TYR A 924 ARG 0.003 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 254 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9103 (pmm) cc_final: 0.8649 (pmm) REVERT: A 58 ILE cc_start: 0.9529 (mt) cc_final: 0.9208 (tp) REVERT: A 100 PHE cc_start: 0.8231 (m-10) cc_final: 0.7913 (m-10) REVERT: A 103 LEU cc_start: 0.9610 (tp) cc_final: 0.9264 (tp) REVERT: A 107 MET cc_start: 0.9566 (mmp) cc_final: 0.9252 (mmp) REVERT: A 188 MET cc_start: 0.8968 (mmm) cc_final: 0.8588 (tpp) REVERT: A 191 GLN cc_start: 0.9373 (tm-30) cc_final: 0.8963 (tm-30) REVERT: A 237 ASP cc_start: 0.8673 (m-30) cc_final: 0.8166 (p0) REVERT: A 278 GLU cc_start: 0.9024 (tp30) cc_final: 0.8804 (mm-30) REVERT: A 331 PHE cc_start: 0.9293 (t80) cc_final: 0.9035 (t80) REVERT: A 335 LEU cc_start: 0.8935 (mt) cc_final: 0.8701 (mt) REVERT: A 359 TYR cc_start: 0.8893 (t80) cc_final: 0.8021 (t80) REVERT: A 438 ARG cc_start: 0.8709 (mtt180) cc_final: 0.8450 (mtt180) REVERT: A 439 LEU cc_start: 0.9585 (mt) cc_final: 0.9332 (mt) REVERT: A 558 ASP cc_start: 0.8719 (m-30) cc_final: 0.8483 (t0) REVERT: A 749 ASN cc_start: 0.9021 (m-40) cc_final: 0.8644 (m-40) REVERT: A 754 LEU cc_start: 0.9175 (mt) cc_final: 0.8921 (mt) REVERT: A 828 ARG cc_start: 0.9004 (tpt170) cc_final: 0.8790 (tpt90) REVERT: A 928 MET cc_start: 0.9129 (mpp) cc_final: 0.8895 (mpp) REVERT: A 938 PHE cc_start: 0.9379 (t80) cc_final: 0.9096 (t80) REVERT: A 953 PHE cc_start: 0.8459 (m-80) cc_final: 0.8255 (m-80) REVERT: A 955 PHE cc_start: 0.8814 (t80) cc_final: 0.8019 (t80) REVERT: A 960 VAL cc_start: 0.9524 (t) cc_final: 0.9316 (t) REVERT: A 1109 LEU cc_start: 0.9390 (mt) cc_final: 0.9075 (mt) REVERT: A 1134 ARG cc_start: 0.8488 (mtp-110) cc_final: 0.8110 (mtp180) outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.1714 time to fit residues: 63.4783 Evaluate side-chains 220 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.2980 chunk 1 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 40.0000 chunk 99 optimal weight: 0.0060 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9166 Z= 0.162 Angle : 0.545 10.111 12393 Z= 0.289 Chirality : 0.040 0.172 1423 Planarity : 0.003 0.042 1578 Dihedral : 4.762 41.441 1274 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % 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: 0.22 (0.25), residues: 1153 helix: 1.18 (0.19), residues: 743 sheet: -0.62 (0.76), residues: 49 loop : -1.98 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 694 HIS 0.004 0.001 HIS A 60 PHE 0.029 0.002 PHE A 934 TYR 0.023 0.001 TYR A 924 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.8861 (pmm) cc_final: 0.8619 (pmm) REVERT: A 58 ILE cc_start: 0.9503 (mt) cc_final: 0.9261 (tp) REVERT: A 66 LEU cc_start: 0.8699 (tp) cc_final: 0.8317 (tp) REVERT: A 67 MET cc_start: 0.9405 (tpt) cc_final: 0.9159 (tpp) REVERT: A 99 MET cc_start: 0.8286 (pmm) cc_final: 0.8081 (pmm) REVERT: A 103 LEU cc_start: 0.9592 (tp) cc_final: 0.9133 (tp) REVERT: A 107 MET cc_start: 0.9578 (mmp) cc_final: 0.9242 (mmp) REVERT: A 160 ASP cc_start: 0.8520 (m-30) cc_final: 0.8247 (m-30) REVERT: A 188 MET cc_start: 0.8815 (mmm) cc_final: 0.8326 (tpp) REVERT: A 191 GLN cc_start: 0.9340 (tm-30) cc_final: 0.8987 (tm-30) REVERT: A 228 TRP cc_start: 0.8786 (m100) cc_final: 0.8343 (m100) REVERT: A 237 ASP cc_start: 0.8660 (m-30) cc_final: 0.8089 (p0) REVERT: A 278 GLU cc_start: 0.8913 (tp30) cc_final: 0.8710 (mm-30) REVERT: A 335 LEU cc_start: 0.8918 (mt) cc_final: 0.8551 (mt) REVERT: A 359 TYR cc_start: 0.8791 (t80) cc_final: 0.7956 (t80) REVERT: A 406 LEU cc_start: 0.8892 (mm) cc_final: 0.8686 (mm) REVERT: A 438 ARG cc_start: 0.8687 (mtt180) cc_final: 0.8271 (mtt180) REVERT: A 498 LYS cc_start: 0.8636 (tptt) cc_final: 0.8271 (ptpt) REVERT: A 506 TYR cc_start: 0.7885 (m-10) cc_final: 0.7451 (m-10) REVERT: A 558 ASP cc_start: 0.8653 (m-30) cc_final: 0.8439 (t0) REVERT: A 749 ASN cc_start: 0.8890 (m-40) cc_final: 0.8537 (m-40) REVERT: A 754 LEU cc_start: 0.9139 (mt) cc_final: 0.8862 (mt) REVERT: A 787 MET cc_start: 0.7825 (mmt) cc_final: 0.7509 (mtt) REVERT: A 872 MET cc_start: 0.7366 (mmp) cc_final: 0.7019 (mmm) REVERT: A 928 MET cc_start: 0.9072 (mpp) cc_final: 0.8805 (mpp) REVERT: A 938 PHE cc_start: 0.9358 (t80) cc_final: 0.9110 (t80) REVERT: A 960 VAL cc_start: 0.9525 (t) cc_final: 0.9293 (t) REVERT: A 1134 ARG cc_start: 0.8436 (mtp-110) cc_final: 0.8062 (mtp180) REVERT: A 1177 LYS cc_start: 0.9164 (ptpt) cc_final: 0.8893 (pttt) outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.1718 time to fit residues: 64.4061 Evaluate side-chains 225 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9166 Z= 0.189 Angle : 0.557 12.790 12393 Z= 0.299 Chirality : 0.041 0.185 1423 Planarity : 0.004 0.072 1578 Dihedral : 4.736 40.128 1274 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 0.19 (0.25), residues: 1153 helix: 1.16 (0.19), residues: 744 sheet: -0.61 (0.75), residues: 49 loop : -1.98 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 694 HIS 0.005 0.001 HIS A 60 PHE 0.027 0.002 PHE A 953 TYR 0.023 0.001 TYR A 924 ARG 0.011 0.000 ARG A 828 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9087 (pmm) cc_final: 0.8569 (pmm) REVERT: A 58 ILE cc_start: 0.9500 (mt) cc_final: 0.9270 (tp) REVERT: A 67 MET cc_start: 0.9406 (tpt) cc_final: 0.9139 (tpp) REVERT: A 100 PHE cc_start: 0.8469 (m-10) cc_final: 0.8171 (m-10) REVERT: A 103 LEU cc_start: 0.9558 (tp) cc_final: 0.9098 (tp) REVERT: A 107 MET cc_start: 0.9576 (mmp) cc_final: 0.9257 (mmp) REVERT: A 160 ASP cc_start: 0.8585 (m-30) cc_final: 0.8322 (m-30) REVERT: A 188 MET cc_start: 0.8838 (mmm) cc_final: 0.8424 (tpp) REVERT: A 191 GLN cc_start: 0.9334 (tm-30) cc_final: 0.8959 (tm-30) REVERT: A 228 TRP cc_start: 0.8818 (m100) cc_final: 0.8347 (m100) REVERT: A 335 LEU cc_start: 0.8907 (mt) cc_final: 0.8581 (mt) REVERT: A 359 TYR cc_start: 0.8798 (t80) cc_final: 0.7951 (t80) REVERT: A 406 LEU cc_start: 0.8888 (mm) cc_final: 0.8681 (mm) REVERT: A 438 ARG cc_start: 0.8799 (mtt180) cc_final: 0.8309 (mtt180) REVERT: A 498 LYS cc_start: 0.8612 (tptt) cc_final: 0.8250 (ptpt) REVERT: A 558 ASP cc_start: 0.8691 (m-30) cc_final: 0.8472 (t0) REVERT: A 749 ASN cc_start: 0.8955 (m-40) cc_final: 0.8578 (m-40) REVERT: A 754 LEU cc_start: 0.9145 (mt) cc_final: 0.8878 (mt) REVERT: A 787 MET cc_start: 0.7859 (mmt) cc_final: 0.7523 (mtt) REVERT: A 872 MET cc_start: 0.7423 (mmp) cc_final: 0.7078 (mmm) REVERT: A 915 MET cc_start: 0.9356 (mtm) cc_final: 0.9109 (mtt) REVERT: A 928 MET cc_start: 0.9072 (mpp) cc_final: 0.8827 (mpp) REVERT: A 938 PHE cc_start: 0.9346 (t80) cc_final: 0.9089 (t80) REVERT: A 953 PHE cc_start: 0.8510 (m-80) cc_final: 0.8252 (m-80) REVERT: A 955 PHE cc_start: 0.8762 (t80) cc_final: 0.7901 (t80) REVERT: A 960 VAL cc_start: 0.9529 (t) cc_final: 0.9303 (t) REVERT: A 1077 GLN cc_start: 0.9043 (mm110) cc_final: 0.8519 (mm110) REVERT: A 1082 PHE cc_start: 0.7508 (m-10) cc_final: 0.7246 (m-10) REVERT: A 1109 LEU cc_start: 0.9368 (mt) cc_final: 0.9006 (mt) REVERT: A 1134 ARG cc_start: 0.8447 (mtp-110) cc_final: 0.8070 (mtp180) REVERT: A 1177 LYS cc_start: 0.9259 (ptpt) cc_final: 0.8940 (pttt) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1692 time to fit residues: 62.6490 Evaluate side-chains 218 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9166 Z= 0.240 Angle : 0.586 12.591 12393 Z= 0.321 Chirality : 0.041 0.197 1423 Planarity : 0.004 0.043 1578 Dihedral : 4.886 39.915 1274 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -0.03 (0.25), residues: 1153 helix: 1.02 (0.19), residues: 736 sheet: -0.62 (0.76), residues: 49 loop : -2.09 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 694 HIS 0.006 0.001 HIS A 60 PHE 0.021 0.002 PHE A 204 TYR 0.035 0.002 TYR A 49 ARG 0.009 0.000 ARG A 828 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9084 (pmm) cc_final: 0.8697 (pmm) REVERT: A 58 ILE cc_start: 0.9515 (mt) cc_final: 0.9219 (tp) REVERT: A 67 MET cc_start: 0.9411 (tpt) cc_final: 0.9139 (tpp) REVERT: A 100 PHE cc_start: 0.8448 (m-10) cc_final: 0.8169 (m-10) REVERT: A 103 LEU cc_start: 0.9563 (tp) cc_final: 0.9081 (tp) REVERT: A 107 MET cc_start: 0.9581 (mmp) cc_final: 0.9247 (mmp) REVERT: A 152 MET cc_start: 0.8729 (tmm) cc_final: 0.8484 (tmm) REVERT: A 160 ASP cc_start: 0.8606 (m-30) cc_final: 0.8291 (m-30) REVERT: A 188 MET cc_start: 0.8841 (mmm) cc_final: 0.8460 (tpp) REVERT: A 191 GLN cc_start: 0.9349 (tm-30) cc_final: 0.8999 (tm-30) REVERT: A 335 LEU cc_start: 0.8973 (mt) cc_final: 0.8654 (mt) REVERT: A 359 TYR cc_start: 0.8795 (t80) cc_final: 0.7907 (t80) REVERT: A 406 LEU cc_start: 0.8931 (mm) cc_final: 0.8700 (mm) REVERT: A 438 ARG cc_start: 0.8813 (mtt180) cc_final: 0.8485 (ttt180) REVERT: A 558 ASP cc_start: 0.8767 (m-30) cc_final: 0.8504 (t0) REVERT: A 749 ASN cc_start: 0.9017 (m-40) cc_final: 0.8652 (m-40) REVERT: A 754 LEU cc_start: 0.9152 (mt) cc_final: 0.8889 (mt) REVERT: A 928 MET cc_start: 0.9096 (mpp) cc_final: 0.8890 (mpp) REVERT: A 938 PHE cc_start: 0.9343 (t80) cc_final: 0.9089 (t80) REVERT: A 953 PHE cc_start: 0.8537 (m-80) cc_final: 0.8226 (m-80) REVERT: A 955 PHE cc_start: 0.8780 (t80) cc_final: 0.7923 (t80) REVERT: A 960 VAL cc_start: 0.9556 (t) cc_final: 0.9341 (t) REVERT: A 1039 ASN cc_start: 0.7407 (p0) cc_final: 0.6768 (p0) REVERT: A 1109 LEU cc_start: 0.9406 (mt) cc_final: 0.9086 (mt) REVERT: A 1134 ARG cc_start: 0.8486 (mtp-110) cc_final: 0.8077 (mtp180) REVERT: A 1177 LYS cc_start: 0.9258 (ptpt) cc_final: 0.8998 (pttt) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1668 time to fit residues: 61.0239 Evaluate side-chains 216 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 75 optimal weight: 0.2980 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 96 optimal weight: 30.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9166 Z= 0.174 Angle : 0.566 12.868 12393 Z= 0.300 Chirality : 0.041 0.187 1423 Planarity : 0.004 0.042 1578 Dihedral : 4.749 37.975 1274 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 0.12 (0.25), residues: 1153 helix: 1.09 (0.19), residues: 742 sheet: -0.54 (0.76), residues: 49 loop : -1.97 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 694 HIS 0.004 0.001 HIS A 60 PHE 0.021 0.002 PHE A 200 TYR 0.024 0.002 TYR A 273 ARG 0.008 0.000 ARG A 828 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9119 (pmm) cc_final: 0.8759 (pmm) REVERT: A 58 ILE cc_start: 0.9511 (mt) cc_final: 0.9284 (tp) REVERT: A 67 MET cc_start: 0.9380 (tpt) cc_final: 0.9089 (tpp) REVERT: A 100 PHE cc_start: 0.8433 (m-10) cc_final: 0.8217 (m-10) REVERT: A 103 LEU cc_start: 0.9549 (tp) cc_final: 0.9014 (tp) REVERT: A 107 MET cc_start: 0.9611 (mmp) cc_final: 0.9215 (mmp) REVERT: A 152 MET cc_start: 0.8692 (tmm) cc_final: 0.8418 (tmm) REVERT: A 160 ASP cc_start: 0.8565 (m-30) cc_final: 0.8216 (m-30) REVERT: A 188 MET cc_start: 0.8857 (mmm) cc_final: 0.8523 (tpp) REVERT: A 191 GLN cc_start: 0.9341 (tm-30) cc_final: 0.8966 (tm-30) REVERT: A 228 TRP cc_start: 0.8811 (m100) cc_final: 0.8313 (m100) REVERT: A 335 LEU cc_start: 0.8896 (mt) cc_final: 0.8579 (mt) REVERT: A 359 TYR cc_start: 0.8700 (t80) cc_final: 0.7904 (t80) REVERT: A 406 LEU cc_start: 0.8924 (mm) cc_final: 0.8702 (mm) REVERT: A 438 ARG cc_start: 0.8788 (mtt180) cc_final: 0.8433 (ttt180) REVERT: A 498 LYS cc_start: 0.8507 (tptt) cc_final: 0.8229 (ptpt) REVERT: A 558 ASP cc_start: 0.8724 (m-30) cc_final: 0.8472 (t0) REVERT: A 749 ASN cc_start: 0.8986 (m-40) cc_final: 0.8610 (m-40) REVERT: A 754 LEU cc_start: 0.9149 (mt) cc_final: 0.8880 (mt) REVERT: A 787 MET cc_start: 0.7248 (mmt) cc_final: 0.6901 (mtt) REVERT: A 928 MET cc_start: 0.9079 (mpp) cc_final: 0.8853 (mpp) REVERT: A 938 PHE cc_start: 0.9345 (t80) cc_final: 0.9135 (t80) REVERT: A 953 PHE cc_start: 0.8448 (m-80) cc_final: 0.8209 (m-80) REVERT: A 955 PHE cc_start: 0.8763 (t80) cc_final: 0.7877 (t80) REVERT: A 960 VAL cc_start: 0.9566 (t) cc_final: 0.9306 (t) REVERT: A 969 ASN cc_start: 0.8861 (m-40) cc_final: 0.8610 (m-40) REVERT: A 1109 LEU cc_start: 0.9386 (mt) cc_final: 0.9051 (mt) REVERT: A 1134 ARG cc_start: 0.8441 (mtp-110) cc_final: 0.8048 (mtp180) REVERT: A 1177 LYS cc_start: 0.9275 (ptpt) cc_final: 0.8990 (pttt) REVERT: A 1231 SER cc_start: 0.9438 (m) cc_final: 0.9036 (m) REVERT: A 1234 GLN cc_start: 0.8506 (tp-100) cc_final: 0.8083 (pt0) outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1813 time to fit residues: 68.0077 Evaluate side-chains 213 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 0.0040 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9166 Z= 0.180 Angle : 0.589 12.701 12393 Z= 0.309 Chirality : 0.041 0.186 1423 Planarity : 0.004 0.042 1578 Dihedral : 4.710 36.651 1274 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1153 helix: 1.15 (0.19), residues: 742 sheet: -0.66 (0.74), residues: 49 loop : -1.92 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 694 HIS 0.004 0.001 HIS A 60 PHE 0.022 0.002 PHE A 200 TYR 0.032 0.002 TYR A 49 ARG 0.007 0.000 ARG A 828 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9082 (pmm) cc_final: 0.8766 (pmm) REVERT: A 49 TYR cc_start: 0.8223 (m-80) cc_final: 0.7867 (m-80) REVERT: A 58 ILE cc_start: 0.9494 (mt) cc_final: 0.9258 (tp) REVERT: A 67 MET cc_start: 0.9380 (tpt) cc_final: 0.9052 (tpp) REVERT: A 100 PHE cc_start: 0.8416 (m-10) cc_final: 0.8207 (m-10) REVERT: A 103 LEU cc_start: 0.9545 (tp) cc_final: 0.8962 (tp) REVERT: A 107 MET cc_start: 0.9613 (mmp) cc_final: 0.9260 (mmm) REVERT: A 110 TYR cc_start: 0.9118 (m-10) cc_final: 0.8848 (m-10) REVERT: A 160 ASP cc_start: 0.8626 (m-30) cc_final: 0.8229 (m-30) REVERT: A 188 MET cc_start: 0.8812 (mmm) cc_final: 0.8431 (tpp) REVERT: A 191 GLN cc_start: 0.9343 (tm-30) cc_final: 0.8971 (tm-30) REVERT: A 206 ARG cc_start: 0.8070 (mmm160) cc_final: 0.7755 (mmm160) REVERT: A 228 TRP cc_start: 0.8872 (m100) cc_final: 0.8382 (m100) REVERT: A 335 LEU cc_start: 0.8885 (mt) cc_final: 0.8602 (mt) REVERT: A 359 TYR cc_start: 0.8671 (t80) cc_final: 0.7904 (t80) REVERT: A 406 LEU cc_start: 0.8908 (mm) cc_final: 0.8674 (mm) REVERT: A 438 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8360 (mtt180) REVERT: A 471 GLN cc_start: 0.8619 (pt0) cc_final: 0.8152 (pm20) REVERT: A 498 LYS cc_start: 0.8496 (tptt) cc_final: 0.8218 (ptpt) REVERT: A 551 ASP cc_start: 0.9047 (t70) cc_final: 0.8816 (t70) REVERT: A 558 ASP cc_start: 0.8749 (m-30) cc_final: 0.8485 (t0) REVERT: A 749 ASN cc_start: 0.8939 (m-40) cc_final: 0.8597 (m-40) REVERT: A 754 LEU cc_start: 0.9138 (mt) cc_final: 0.8862 (mt) REVERT: A 928 MET cc_start: 0.9063 (mpp) cc_final: 0.8841 (mpp) REVERT: A 938 PHE cc_start: 0.9344 (t80) cc_final: 0.9081 (t80) REVERT: A 953 PHE cc_start: 0.8450 (m-80) cc_final: 0.8226 (m-80) REVERT: A 955 PHE cc_start: 0.8732 (t80) cc_final: 0.7802 (t80) REVERT: A 960 VAL cc_start: 0.9549 (t) cc_final: 0.9290 (t) REVERT: A 969 ASN cc_start: 0.8761 (m-40) cc_final: 0.8427 (m-40) REVERT: A 1109 LEU cc_start: 0.9406 (mt) cc_final: 0.9077 (mt) REVERT: A 1134 ARG cc_start: 0.8433 (mtp-110) cc_final: 0.8063 (mtp180) REVERT: A 1177 LYS cc_start: 0.9281 (ptpt) cc_final: 0.8996 (pttt) REVERT: A 1231 SER cc_start: 0.9430 (m) cc_final: 0.9014 (m) REVERT: A 1234 GLN cc_start: 0.8543 (tp-100) cc_final: 0.8185 (pt0) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1650 time to fit residues: 60.8793 Evaluate side-chains 222 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9990 chunk 51 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 105 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 70 optimal weight: 0.0870 chunk 55 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9166 Z= 0.168 Angle : 0.580 12.951 12393 Z= 0.302 Chirality : 0.041 0.185 1423 Planarity : 0.003 0.043 1578 Dihedral : 4.624 35.871 1274 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: 0.30 (0.25), residues: 1153 helix: 1.22 (0.19), residues: 745 sheet: -0.65 (0.74), residues: 49 loop : -1.89 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 694 HIS 0.004 0.001 HIS A 60 PHE 0.022 0.002 PHE A 200 TYR 0.029 0.002 TYR A 49 ARG 0.003 0.000 ARG A 828 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.9046 (pmm) cc_final: 0.8782 (pmm) REVERT: A 50 MET cc_start: 0.8688 (mtp) cc_final: 0.8234 (mmm) REVERT: A 58 ILE cc_start: 0.9495 (mt) cc_final: 0.9271 (tp) REVERT: A 67 MET cc_start: 0.9371 (tpt) cc_final: 0.9034 (tpp) REVERT: A 100 PHE cc_start: 0.8387 (m-10) cc_final: 0.8128 (m-10) REVERT: A 103 LEU cc_start: 0.9530 (tp) cc_final: 0.9127 (tp) REVERT: A 107 MET cc_start: 0.9609 (mmp) cc_final: 0.9306 (mmp) REVERT: A 160 ASP cc_start: 0.8620 (m-30) cc_final: 0.8222 (m-30) REVERT: A 191 GLN cc_start: 0.9331 (tm-30) cc_final: 0.8953 (tm-30) REVERT: A 228 TRP cc_start: 0.8840 (m100) cc_final: 0.8330 (m100) REVERT: A 359 TYR cc_start: 0.8638 (t80) cc_final: 0.7913 (t80) REVERT: A 406 LEU cc_start: 0.8888 (mm) cc_final: 0.8654 (mm) REVERT: A 438 ARG cc_start: 0.8730 (mtt180) cc_final: 0.8353 (ttt180) REVERT: A 471 GLN cc_start: 0.8611 (pt0) cc_final: 0.8156 (pm20) REVERT: A 482 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8780 (mt-10) REVERT: A 483 ASN cc_start: 0.8894 (m110) cc_final: 0.8653 (m110) REVERT: A 498 LYS cc_start: 0.8493 (tptt) cc_final: 0.8220 (ptpt) REVERT: A 551 ASP cc_start: 0.9048 (t70) cc_final: 0.8845 (t70) REVERT: A 558 ASP cc_start: 0.8739 (m-30) cc_final: 0.8475 (t0) REVERT: A 749 ASN cc_start: 0.8924 (m-40) cc_final: 0.8578 (m-40) REVERT: A 754 LEU cc_start: 0.9130 (mt) cc_final: 0.8856 (mt) REVERT: A 787 MET cc_start: 0.7595 (mmt) cc_final: 0.7273 (mtt) REVERT: A 828 ARG cc_start: 0.9074 (mmm160) cc_final: 0.8383 (tpp80) REVERT: A 872 MET cc_start: 0.7427 (mmp) cc_final: 0.7094 (mmm) REVERT: A 928 MET cc_start: 0.9031 (mpp) cc_final: 0.8807 (mpp) REVERT: A 938 PHE cc_start: 0.9341 (t80) cc_final: 0.9090 (t80) REVERT: A 953 PHE cc_start: 0.8505 (m-80) cc_final: 0.8219 (m-80) REVERT: A 955 PHE cc_start: 0.8763 (t80) cc_final: 0.7860 (t80) REVERT: A 965 MET cc_start: 0.8589 (tmm) cc_final: 0.7931 (tmm) REVERT: A 1109 LEU cc_start: 0.9376 (mt) cc_final: 0.9044 (mt) REVERT: A 1177 LYS cc_start: 0.9283 (ptpt) cc_final: 0.9001 (pttt) REVERT: A 1205 GLU cc_start: 0.8844 (tt0) cc_final: 0.8625 (tp30) REVERT: A 1231 SER cc_start: 0.9425 (m) cc_final: 0.9011 (m) REVERT: A 1234 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8187 (pt0) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.1648 time to fit residues: 62.6124 Evaluate side-chains 216 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 838 ASN ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.120444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.088069 restraints weight = 24031.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.091454 restraints weight = 14556.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093904 restraints weight = 10247.304| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9166 Z= 0.196 Angle : 0.582 12.615 12393 Z= 0.308 Chirality : 0.041 0.179 1423 Planarity : 0.004 0.077 1578 Dihedral : 4.663 35.576 1274 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 0.23 (0.25), residues: 1153 helix: 1.18 (0.19), residues: 739 sheet: -0.71 (0.73), residues: 49 loop : -1.89 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 694 HIS 0.005 0.001 HIS A 60 PHE 0.022 0.002 PHE A 200 TYR 0.023 0.002 TYR A 924 ARG 0.018 0.000 ARG A 828 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2095.40 seconds wall clock time: 345 minutes 10.40 seconds (20710.40 seconds total)