Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 11 02:14:39 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/08_2023/7zk9_14759_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/08_2023/7zk9_14759.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/08_2023/7zk9_14759_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/08_2023/7zk9_14759_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/08_2023/7zk9_14759_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/08_2023/7zk9_14759.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/08_2023/7zk9_14759.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/08_2023/7zk9_14759_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk9_14759/08_2023/7zk9_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 5.09, per 1000 atoms: 0.57 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: 3.71 Conformation dependent library (CDL) restraints added in 1.4 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: 2.11 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: 2.73 Time building geometry restraints manager: 4.00 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=" C04 JIZ A1301 " pdb=" S01 JIZ A1301 " ideal model delta sigma weight residual 1.322 1.576 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C14 JIZ A1301 " pdb=" S03 JIZ A1301 " ideal model delta sigma weight residual 1.321 1.565 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C03 JIZ A1301 " pdb=" N02 JIZ A1301 " ideal model delta sigma weight residual 1.461 1.638 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" C08 JIZ A1301 " pdb=" N04 JIZ A1301 " ideal model delta sigma weight residual 1.779 1.615 0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" C13 JIZ A1301 " pdb=" N06 JIZ A1301 " ideal model delta sigma weight residual 1.458 1.613 -0.155 2.00e-02 2.50e+03 6.02e+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=" 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=" C GLU A 968 " pdb=" N ASN A 969 " pdb=" CA ASN A 969 " ideal model delta sigma weight residual 120.68 112.22 8.46 1.70e+00 3.46e-01 2.47e+01 angle pdb=" N LEU A 55 " pdb=" CA LEU A 55 " pdb=" C LEU A 55 " ideal model delta sigma weight residual 111.28 106.17 5.11 1.09e+00 8.42e-01 2.20e+01 angle pdb=" N ILE A1150 " pdb=" CA ILE A1150 " pdb=" C ILE A1150 " ideal model delta sigma weight residual 111.77 106.92 4.85 1.04e+00 9.25e-01 2.17e+01 ... (remaining 12388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4944 17.61 - 35.22: 404 35.22 - 52.82: 82 52.82 - 70.43: 9 70.43 - 88.04: 8 Dihedral angle restraints: 5447 sinusoidal: 2136 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 5444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1073 0.058 - 0.116: 249 0.116 - 0.174: 62 0.174 - 0.232: 30 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: 1.410 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: 5.390 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.650 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.750 ------------------------------------------------------------------------------- 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 : 0.008 0.254 9166 Z= 0.494 Angle : 0.980 13.969 12393 Z= 0.656 Chirality : 0.062 0.290 1423 Planarity : 0.004 0.039 1578 Dihedral : 13.540 88.038 3325 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 % 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 *********************** 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 : 1.010 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 outliers start: 7 outliers final: 2 residues processed: 278 average time/residue: 0.1732 time to fit residues: 70.0950 Evaluate side-chains 226 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 224 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0784 time to fit residues: 1.5910 ------------------------------------------------------------------------------- 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: 0.9980 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: 1.5386 ------------------------------------------------------------------------------- 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: 0.7870 moved from start: 0.1362 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= 0.197 Angle : 0.592 9.267 12393 Z= 0.315 Chirality : 0.041 0.154 1423 Planarity : 0.004 0.053 1578 Dihedral : 4.451 32.773 1245 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1153 helix: 1.21 (0.19), residues: 742 sheet: -0.86 (0.71), residues: 49 loop : -2.15 (0.31), residues: 362 *********************** 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 258 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 258 average time/residue: 0.1695 time to fit residues: 64.2651 Evaluate side-chains 218 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.402 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4014 ------------------------------------------------------------------------------- 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: 20.0000 chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 83 optimal weight: 0.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** 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: 0.8005 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 9166 Z= 0.341 Angle : 0.679 10.759 12393 Z= 0.375 Chirality : 0.043 0.181 1423 Planarity : 0.005 0.052 1578 Dihedral : 4.651 31.777 1245 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.32 % 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: -0.42 (0.24), residues: 1153 helix: 0.69 (0.18), residues: 737 sheet: -0.85 (0.72), residues: 49 loop : -2.19 (0.31), residues: 367 *********************** 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 254 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 251 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 253 average time/residue: 0.1737 time to fit residues: 64.6059 Evaluate side-chains 217 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0986 time to fit residues: 1.5731 ------------------------------------------------------------------------------- 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: 10.0000 chunk 78 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 29 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS ** A 717 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 9166 Z= 0.228 Angle : 0.623 9.782 12393 Z= 0.332 Chirality : 0.042 0.179 1423 Planarity : 0.004 0.043 1578 Dihedral : 4.630 32.543 1245 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1153 helix: 0.92 (0.19), residues: 738 sheet: -0.74 (0.74), residues: 49 loop : -2.21 (0.30), residues: 366 *********************** 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 257 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.1793 time to fit residues: 68.2264 Evaluate side-chains 213 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6106 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 0.0270 chunk 76 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 40.0000 chunk 99 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 37 optimal weight: 7.9990 overall best weight: 3.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9166 Z= 0.284 Angle : 0.650 11.017 12393 Z= 0.352 Chirality : 0.043 0.163 1423 Planarity : 0.004 0.044 1578 Dihedral : 4.714 32.959 1245 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1153 helix: 0.71 (0.18), residues: 735 sheet: -0.75 (0.75), residues: 49 loop : -2.22 (0.30), residues: 369 *********************** 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 248 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 247 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.1780 time to fit residues: 64.7244 Evaluate side-chains 212 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3734 ------------------------------------------------------------------------------- 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: 0.9990 chunk 21 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 9166 Z= 0.170 Angle : 0.613 10.319 12393 Z= 0.318 Chirality : 0.042 0.191 1423 Planarity : 0.004 0.042 1578 Dihedral : 4.561 33.476 1245 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 0.00 % 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: 0.00 (0.25), residues: 1153 helix: 1.02 (0.19), residues: 741 sheet: -0.23 (0.81), residues: 44 loop : -2.10 (0.31), residues: 368 *********************** 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 263 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1736 time to fit residues: 67.1622 Evaluate side-chains 223 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.016 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3864 ------------------------------------------------------------------------------- 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: 9.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN ** 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: 0.7920 moved from start: 0.2876 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= 0.203 Angle : 0.617 10.369 12393 Z= 0.325 Chirality : 0.042 0.172 1423 Planarity : 0.004 0.044 1578 Dihedral : 4.582 33.612 1245 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.00 % 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 (0.25), residues: 1153 helix: 0.95 (0.19), residues: 737 sheet: -0.19 (0.81), residues: 44 loop : -2.14 (0.30), residues: 372 *********************** 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 255 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 255 average time/residue: 0.1751 time to fit residues: 65.3451 Evaluate side-chains 217 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4187 ------------------------------------------------------------------------------- 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: 5.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 100 optimal weight: 0.0070 chunk 106 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 9166 Z= 0.220 Angle : 0.628 10.927 12393 Z= 0.332 Chirality : 0.043 0.205 1423 Planarity : 0.004 0.044 1578 Dihedral : 4.618 33.490 1245 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 0.00 % 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 (0.24), residues: 1153 helix: 0.94 (0.19), residues: 735 sheet: -0.22 (0.80), residues: 44 loop : -2.14 (0.30), residues: 374 *********************** 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 256 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1799 time to fit residues: 68.4191 Evaluate side-chains 213 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.027 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4160 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 ASN ** A 834 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: 0.7974 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 9166 Z= 0.280 Angle : 0.671 10.943 12393 Z= 0.361 Chirality : 0.044 0.202 1423 Planarity : 0.004 0.047 1578 Dihedral : 4.759 33.177 1245 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.00 % 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: -0.39 (0.24), residues: 1153 helix: 0.70 (0.19), residues: 736 sheet: -0.75 (0.73), residues: 49 loop : -2.14 (0.31), residues: 368 *********************** 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 : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1769 time to fit residues: 65.7621 Evaluate side-chains 218 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4143 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 105 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9166 Z= 0.206 Angle : 0.646 11.218 12393 Z= 0.335 Chirality : 0.043 0.193 1423 Planarity : 0.004 0.044 1578 Dihedral : 4.696 33.180 1245 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer Outliers : 0.00 % 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: -0.17 (0.25), residues: 1153 helix: 0.86 (0.19), residues: 740 sheet: -0.38 (0.78), residues: 44 loop : -2.10 (0.31), residues: 369 ********************** 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 257 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.1794 time to fit residues: 68.6838 Evaluate side-chains 218 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3087 ------------------------------------------------------------------------------- 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: 2.9990 chunk 13 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 717 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 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 = 0.3835 r_free = 0.3835 target = 0.121744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.089430 restraints weight = 23559.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092922 restraints weight = 14217.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095346 restraints weight = 9945.188| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9166 Z= 0.180 Angle : 0.630 10.502 12393 Z= 0.324 Chirality : 0.043 0.193 1423 Planarity : 0.004 0.044 1578 Dihedral : 4.697 33.546 1245 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.00 % 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 (0.25), residues: 1153 helix: 0.91 (0.19), residues: 740 sheet: -0.71 (0.74), residues: 49 loop : -2.02 (0.31), residues: 364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2020.92 seconds wall clock time: 37 minutes 25.50 seconds (2245.50 seconds total)