Starting phenix.real_space_refine on Thu Mar 14 14:09:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/03_2024/7zkb_14761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/03_2024/7zkb_14761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/03_2024/7zkb_14761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/03_2024/7zkb_14761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/03_2024/7zkb_14761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/03_2024/7zkb_14761_updated.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.023 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 39 5.16 5 C 5806 2.51 5 N 1541 2.21 5 O 1657 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 497": "OE1" <-> "OE2" Residue "A GLU 885": "OE1" <-> "OE2" Residue "A GLU 887": "OE1" <-> "OE2" Residue "A GLU 1013": "OE1" <-> "OE2" Residue "A GLU 1207": "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: 9043 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 9043 Unusual residues: {'JIZ': 1, 'JJI': 1} Classifications: {'peptide': 1157, 'undetermined': 2} Link IDs: {'PTRANS': 29, 'TRANS': 1127, None: 2} Not linked: pdbres="LYS A1260 " pdbres="JIZ A1401 " Not linked: pdbres="JIZ A1401 " pdbres="JJI A1402 " Chain breaks: 1 Time building chain proxies: 4.88, per 1000 atoms: 0.54 Number of scatterers: 9043 At special positions: 0 Unit cell: (77.004, 112.158, 148.149, 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 39 16.00 O 1657 8.00 N 1541 7.00 C 5806 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.6 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: 36 helices and 3 sheets defined 59.6% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 44 through 81 removed outlier: 4.290A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 99 through 151 Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 165 through 206 removed outlier: 4.025A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLN A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 255 Proline residue: A 219 - end of helix removed outlier: 3.672A 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 266 through 318 removed outlier: 4.250A pdb=" N GLU A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ARG A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N LEU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 364 removed outlier: 3.512A pdb=" N VAL A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N SER A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Proline residue: A 346 - end of helix Processing helix chain 'A' and resid 431 through 434 No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 493 through 501 Processing helix chain 'A' and resid 529 through 543 removed outlier: 3.925A pdb=" N ARG A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.617A pdb=" N GLY A 575 " --> pdb=" O LYS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 590 removed outlier: 3.934A pdb=" N ASN A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 586 through 590' Processing helix chain 'A' and resid 697 through 700 No H-bonds generated for 'chain 'A' and resid 697 through 700' Processing helix chain 'A' and resid 704 through 736 removed outlier: 4.717A pdb=" N VAL A 709 " --> pdb=" O PRO A 705 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY A 710 " --> pdb=" O TYR A 706 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 711 " --> pdb=" O PHE A 707 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU A 720 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 3.804A pdb=" N PHE A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 800 removed outlier: 3.956A pdb=" N LYS A 775 " --> pdb=" O PHE A 771 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP A 796 " --> pdb=" O MET A 792 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A 797 " --> pdb=" O LEU A 793 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N SER A 798 " --> pdb=" O ARG A 794 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 800 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 815 Processing helix chain 'A' and resid 818 through 849 removed outlier: 3.607A pdb=" N GLY A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ARG A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 829 " --> pdb=" O THR A 825 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 898 Proline residue: A 862 - end of helix removed outlier: 3.809A pdb=" N LYS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LYS A 884 " --> pdb=" O LEU A 880 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 889 " --> pdb=" O GLU A 885 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE A 892 " --> pdb=" O GLY A 888 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU A 895 " --> pdb=" O LYS A 891 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 967 through 990 removed outlier: 3.507A pdb=" N GLY A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1009 Processing helix chain 'A' and resid 1073 through 1078 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1102 through 1108 removed outlier: 3.648A pdb=" N GLN A1108 " --> pdb=" O TRP A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'A' and resid 1151 through 1154 No H-bonds generated for 'chain 'A' and resid 1151 through 1154' Processing helix chain 'A' and resid 1176 through 1187 Processing helix chain 'A' and resid 1205 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 1109 through 1112 removed outlier: 7.333A pdb=" N ILE A1192 " --> pdb=" O GLY A1110 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N VAL A1112 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A1194 " --> pdb=" O VAL A1112 " (cutoff:3.500A) 496 hydrogen bonds defined for protein. 1485 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: 2.54 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 1481 1.31 - 1.46: 2772 1.46 - 1.60: 4886 1.60 - 1.74: 12 1.74 - 1.89: 63 Bond restraints: 9214 Sorted by residual: bond pdb=" N2 JJI A1402 " pdb=" O22 JJI A1402 " ideal model delta sigma weight residual 1.204 1.405 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" N4 JJI A1402 " pdb=" O41 JJI A1402 " ideal model delta sigma weight residual 1.206 1.404 -0.198 2.00e-02 2.50e+03 9.84e+01 bond pdb=" N2 JJI A1402 " pdb=" O21 JJI A1402 " ideal model delta sigma weight residual 1.206 1.404 -0.198 2.00e-02 2.50e+03 9.76e+01 bond pdb=" N4 JJI A1402 " pdb=" O42 JJI A1402 " ideal model delta sigma weight residual 1.207 1.403 -0.196 2.00e-02 2.50e+03 9.62e+01 bond pdb=" S JJI A1402 " pdb=" S04 JJI A1402 " ideal model delta sigma weight residual 2.053 1.888 0.165 2.00e-02 2.50e+03 6.83e+01 ... (remaining 9209 not shown) Histogram of bond angle deviations from ideal: 95.66 - 103.38: 87 103.38 - 111.10: 3383 111.10 - 118.81: 4122 118.81 - 126.53: 4769 126.53 - 134.25: 100 Bond angle restraints: 12461 Sorted by residual: angle pdb=" N TYR A 306 " pdb=" CA TYR A 306 " pdb=" C TYR A 306 " ideal model delta sigma weight residual 111.28 98.42 12.86 1.09e+00 8.42e-01 1.39e+02 angle pdb=" N VAL A 249 " pdb=" CA VAL A 249 " pdb=" C VAL A 249 " ideal model delta sigma weight residual 110.62 102.65 7.97 1.02e+00 9.61e-01 6.11e+01 angle pdb=" C18 JJI A1402 " pdb=" S04 JJI A1402 " pdb=" S JJI A1402 " ideal model delta sigma weight residual 102.75 122.96 -20.21 3.00e+00 1.11e-01 4.54e+01 angle pdb=" O ALA A 244 " pdb=" C ALA A 244 " pdb=" N LYS A 245 " ideal model delta sigma weight residual 122.22 114.95 7.27 1.17e+00 7.31e-01 3.86e+01 angle pdb=" C13 JIZ A1401 " pdb=" C15 JIZ A1401 " pdb=" N01 JIZ A1401 " ideal model delta sigma weight residual 114.63 131.99 -17.36 3.00e+00 1.11e-01 3.35e+01 ... (remaining 12456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 5105 22.47 - 44.94: 326 44.94 - 67.40: 32 67.40 - 89.87: 17 89.87 - 112.34: 12 Dihedral angle restraints: 5492 sinusoidal: 2181 harmonic: 3311 Sorted by residual: dihedral pdb=" C PHE A 339 " pdb=" N PHE A 339 " pdb=" CA PHE A 339 " pdb=" CB PHE A 339 " ideal model delta harmonic sigma weight residual -122.60 -111.42 -11.18 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" C ASN A 276 " pdb=" N ASN A 276 " pdb=" CA ASN A 276 " pdb=" CB ASN A 276 " ideal model delta harmonic sigma weight residual -122.60 -133.39 10.79 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" CA GLU A1139 " pdb=" C GLU A1139 " pdb=" N GLU A1140 " pdb=" CA GLU A1140 " ideal model delta harmonic sigma weight residual 180.00 160.79 19.21 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 5489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1186 0.071 - 0.143: 186 0.143 - 0.214: 38 0.214 - 0.286: 9 0.286 - 0.357: 7 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CA LYS A 245 " pdb=" N LYS A 245 " pdb=" C LYS A 245 " pdb=" CB LYS A 245 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CA PHE A 339 " pdb=" N PHE A 339 " pdb=" C PHE A 339 " pdb=" CB PHE A 339 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA TYR A 306 " pdb=" N TYR A 306 " pdb=" C TYR A 306 " pdb=" CB TYR A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 1423 not shown) Planarity restraints: 1586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 244 " -0.026 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C ALA A 244 " 0.085 2.00e-02 2.50e+03 pdb=" O ALA A 244 " -0.030 2.00e-02 2.50e+03 pdb=" N LYS A 245 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 247 " 0.017 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C GLY A 247 " -0.060 2.00e-02 2.50e+03 pdb=" O GLY A 247 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA A 248 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 301 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C LEU A 301 " 0.059 2.00e-02 2.50e+03 pdb=" O LEU A 301 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE A 302 " -0.020 2.00e-02 2.50e+03 ... (remaining 1583 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1453 2.76 - 3.29: 9842 3.29 - 3.83: 14937 3.83 - 4.36: 16962 4.36 - 4.90: 27249 Nonbonded interactions: 70443 Sorted by model distance: nonbonded pdb=" O TYR A1129 " pdb=" ND2 ASN A1132 " model vdw 2.224 2.520 nonbonded pdb=" O GLY A 427 " pdb=" OG1 THR A 431 " model vdw 2.231 2.440 nonbonded pdb=" OG SER A1122 " pdb=" O TYR A1161 " model vdw 2.243 2.440 nonbonded pdb=" O ALA A 79 " pdb=" CG GLN A 83 " model vdw 2.246 3.440 nonbonded pdb=" O MET A 74 " pdb=" OG SER A 77 " model vdw 2.260 2.440 ... (remaining 70438 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: 0.980 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: 0.000 Extract box with map and model: 4.950 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.110 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 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 0.201 9214 Z= 0.490 Angle : 1.045 20.208 12461 Z= 0.643 Chirality : 0.061 0.357 1426 Planarity : 0.005 0.062 1586 Dihedral : 15.447 112.340 3370 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 0.21 % Allowed : 1.80 % Favored : 97.99 % Cbeta Deviations : 0.19 % 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: 0.07 (0.26), residues: 1153 helix: 1.03 (0.20), residues: 711 sheet: -0.11 (0.83), residues: 42 loop : -1.74 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 704 HIS 0.004 0.000 HIS A1003 PHE 0.016 0.001 PHE A1038 TYR 0.017 0.002 TYR A 113 ARG 0.006 0.000 ARG A1134 *********************** 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 246 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.7500 (tpp) cc_final: 0.7296 (mmt) REVERT: A 127 ILE cc_start: 0.8749 (mt) cc_final: 0.8518 (mt) REVERT: A 152 MET cc_start: 0.7790 (tpp) cc_final: 0.7519 (tmm) REVERT: A 174 ASP cc_start: 0.7962 (m-30) cc_final: 0.7193 (m-30) REVERT: A 259 THR cc_start: 0.9561 (p) cc_final: 0.9256 (p) REVERT: A 263 PHE cc_start: 0.8357 (m-80) cc_final: 0.7986 (m-80) REVERT: A 316 LEU cc_start: 0.8518 (mt) cc_final: 0.7809 (mt) REVERT: A 364 ILE cc_start: 0.8642 (mp) cc_final: 0.8133 (tp) REVERT: A 765 THR cc_start: 0.8773 (m) cc_final: 0.8571 (m) REVERT: A 913 GLU cc_start: 0.7085 (tt0) cc_final: 0.6694 (tt0) REVERT: A 968 GLU cc_start: 0.7206 (pp20) cc_final: 0.6880 (pp20) REVERT: A 1062 LEU cc_start: 0.9358 (tp) cc_final: 0.9077 (tp) outliers start: 2 outliers final: 1 residues processed: 246 average time/residue: 0.1845 time to fit residues: 64.6311 Evaluate side-chains 204 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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: 10.0000 chunk 87 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.0470 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN A 737 ASN ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN A1253 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9214 Z= 0.181 Angle : 0.591 7.641 12461 Z= 0.308 Chirality : 0.040 0.199 1426 Planarity : 0.004 0.068 1586 Dihedral : 12.494 108.190 1289 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.21 % Allowed : 2.96 % Favored : 96.83 % 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 (0.26), residues: 1153 helix: 1.11 (0.20), residues: 723 sheet: 0.22 (0.84), residues: 36 loop : -1.92 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 704 HIS 0.002 0.001 HIS A 241 PHE 0.029 0.002 PHE A 755 TYR 0.015 0.002 TYR A 306 ARG 0.006 0.000 ARG A 485 *********************** 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 237 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7954 (tpp) cc_final: 0.7547 (mmm) REVERT: A 197 PHE cc_start: 0.8278 (m-80) cc_final: 0.8025 (m-80) REVERT: A 259 THR cc_start: 0.9588 (p) cc_final: 0.9317 (p) REVERT: A 263 PHE cc_start: 0.8422 (m-80) cc_final: 0.8077 (m-80) REVERT: A 720 LEU cc_start: 0.9445 (mm) cc_final: 0.9219 (mm) REVERT: A 765 THR cc_start: 0.8781 (m) cc_final: 0.8567 (m) REVERT: A 785 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7883 (ttp-170) REVERT: A 813 ARG cc_start: 0.8068 (tpt170) cc_final: 0.7800 (ttm170) REVERT: A 915 MET cc_start: 0.7822 (mpp) cc_final: 0.7483 (mpp) REVERT: A 968 GLU cc_start: 0.7170 (pp20) cc_final: 0.6800 (pp20) REVERT: A 1006 ARG cc_start: 0.7564 (ttt90) cc_final: 0.7268 (ttt90) REVERT: A 1020 GLN cc_start: 0.8069 (pp30) cc_final: 0.7797 (pp30) REVERT: A 1062 LEU cc_start: 0.9247 (tp) cc_final: 0.9031 (tp) REVERT: A 1084 ASP cc_start: 0.8677 (p0) cc_final: 0.7511 (t0) REVERT: A 1121 ARG cc_start: 0.6023 (tpt170) cc_final: 0.5743 (tpt170) REVERT: A 1209 VAL cc_start: 0.9106 (t) cc_final: 0.8855 (p) REVERT: A 1211 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8870 (pp30) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1847 time to fit residues: 62.0366 Evaluate side-chains 195 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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: 30.0000 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 113 optimal weight: 0.2980 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 83 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN A 583 HIS ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 GLN A 878 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9214 Z= 0.157 Angle : 0.575 11.116 12461 Z= 0.298 Chirality : 0.040 0.162 1426 Planarity : 0.003 0.052 1586 Dihedral : 11.679 107.444 1289 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.21 % Allowed : 3.91 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.26 (0.26), residues: 1153 helix: 1.25 (0.20), residues: 720 sheet: 0.12 (0.84), residues: 36 loop : -1.90 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 704 HIS 0.003 0.000 HIS A1003 PHE 0.017 0.001 PHE A 331 TYR 0.017 0.001 TYR A 114 ARG 0.005 0.000 ARG A 794 *********************** 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 231 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 229 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASP cc_start: 0.7685 (m-30) cc_final: 0.7365 (m-30) REVERT: A 197 PHE cc_start: 0.8349 (m-80) cc_final: 0.8149 (m-80) REVERT: A 259 THR cc_start: 0.9589 (p) cc_final: 0.9317 (p) REVERT: A 263 PHE cc_start: 0.8448 (m-80) cc_final: 0.8057 (m-80) REVERT: A 374 PHE cc_start: 0.8074 (m-80) cc_final: 0.7666 (t80) REVERT: A 720 LEU cc_start: 0.9432 (mm) cc_final: 0.9220 (mm) REVERT: A 765 THR cc_start: 0.8760 (m) cc_final: 0.8555 (m) REVERT: A 968 GLU cc_start: 0.7118 (pp20) cc_final: 0.6711 (pp20) REVERT: A 1006 ARG cc_start: 0.7504 (ttt90) cc_final: 0.7211 (ttt90) REVERT: A 1084 ASP cc_start: 0.8606 (p0) cc_final: 0.7424 (t0) outliers start: 2 outliers final: 0 residues processed: 231 average time/residue: 0.1802 time to fit residues: 60.0614 Evaluate side-chains 192 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.081 ------------------------------------------------------------------------------- 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: 4.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 0.0870 chunk 111 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 29 optimal weight: 0.0970 chunk 92 optimal weight: 0.0470 overall best weight: 0.9656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9214 Z= 0.167 Angle : 0.566 10.241 12461 Z= 0.293 Chirality : 0.041 0.263 1426 Planarity : 0.003 0.047 1586 Dihedral : 11.158 105.297 1289 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.11 % Allowed : 4.01 % Favored : 95.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.36 (0.26), residues: 1153 helix: 1.34 (0.20), residues: 718 sheet: 0.23 (0.84), residues: 36 loop : -1.87 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 704 HIS 0.002 0.001 HIS A1003 PHE 0.021 0.002 PHE A 953 TYR 0.034 0.002 TYR A 114 ARG 0.005 0.000 ARG A 794 *********************** 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 228 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 ASP cc_start: 0.7737 (m-30) cc_final: 0.7423 (m-30) REVERT: A 259 THR cc_start: 0.9579 (p) cc_final: 0.9283 (p) REVERT: A 276 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8113 (t0) REVERT: A 334 VAL cc_start: 0.9021 (t) cc_final: 0.8655 (m) REVERT: A 374 PHE cc_start: 0.8080 (m-80) cc_final: 0.7551 (t80) REVERT: A 436 MET cc_start: 0.9286 (mmp) cc_final: 0.9042 (mmm) REVERT: A 720 LEU cc_start: 0.9454 (mm) cc_final: 0.9213 (mm) REVERT: A 765 THR cc_start: 0.8744 (m) cc_final: 0.8527 (m) REVERT: A 912 PHE cc_start: 0.8138 (m-10) cc_final: 0.7785 (m-80) REVERT: A 915 MET cc_start: 0.8039 (mpp) cc_final: 0.7348 (mpp) REVERT: A 968 GLU cc_start: 0.7073 (pp20) cc_final: 0.6690 (pp20) REVERT: A 1006 ARG cc_start: 0.7486 (ttt90) cc_final: 0.7216 (ttt90) REVERT: A 1062 LEU cc_start: 0.9262 (tp) cc_final: 0.9016 (tp) REVERT: A 1084 ASP cc_start: 0.8608 (p0) cc_final: 0.8303 (p0) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.1821 time to fit residues: 59.7596 Evaluate side-chains 190 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 20.0000 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 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS A 566 GLN A 737 ASN A 834 GLN A 878 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9214 Z= 0.276 Angle : 0.658 7.681 12461 Z= 0.350 Chirality : 0.042 0.213 1426 Planarity : 0.005 0.059 1586 Dihedral : 11.272 98.883 1289 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.11 % Allowed : 3.80 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.96 (0.19), residues: 715 sheet: 0.33 (0.85), residues: 35 loop : -2.11 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 704 HIS 0.003 0.001 HIS A 141 PHE 0.035 0.003 PHE A 78 TYR 0.019 0.002 TYR A 306 ARG 0.007 0.001 ARG A 745 *********************** 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 224 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.8727 (tp) cc_final: 0.8276 (tp) REVERT: A 174 ASP cc_start: 0.7993 (m-30) cc_final: 0.7630 (m-30) REVERT: A 197 PHE cc_start: 0.8444 (m-80) cc_final: 0.8149 (m-80) REVERT: A 278 GLU cc_start: 0.8594 (tt0) cc_final: 0.7850 (tp30) REVERT: A 281 LYS cc_start: 0.8529 (pttp) cc_final: 0.7209 (pttp) REVERT: A 295 MET cc_start: 0.8179 (ttm) cc_final: 0.7935 (ttt) REVERT: A 306 TYR cc_start: 0.8243 (t80) cc_final: 0.7974 (t80) REVERT: A 436 MET cc_start: 0.9335 (mmp) cc_final: 0.9071 (mmm) REVERT: A 485 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7620 (mtm110) REVERT: A 720 LEU cc_start: 0.9503 (mm) cc_final: 0.9204 (mm) REVERT: A 765 THR cc_start: 0.8788 (m) cc_final: 0.8554 (m) REVERT: A 912 PHE cc_start: 0.8214 (m-10) cc_final: 0.7858 (m-80) REVERT: A 915 MET cc_start: 0.8257 (mpp) cc_final: 0.7318 (mpp) REVERT: A 1006 ARG cc_start: 0.7588 (ttt90) cc_final: 0.7195 (ttt90) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1833 time to fit residues: 58.9805 Evaluate side-chains 191 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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: 10.0000 chunk 21 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 30.0000 chunk 92 optimal weight: 0.0770 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN A 394 HIS A 566 GLN A 878 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9214 Z= 0.254 Angle : 0.629 7.804 12461 Z= 0.338 Chirality : 0.041 0.185 1426 Planarity : 0.004 0.065 1586 Dihedral : 11.071 98.623 1289 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.11 (0.25), residues: 1153 helix: 0.99 (0.19), residues: 709 sheet: 0.19 (0.84), residues: 35 loop : -2.04 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 158 HIS 0.003 0.001 HIS A 141 PHE 0.022 0.002 PHE A 78 TYR 0.021 0.002 TYR A1017 ARG 0.004 0.000 ARG A1188 *********************** 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 220 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.8780 (tp) cc_final: 0.8416 (tp) REVERT: A 174 ASP cc_start: 0.7996 (m-30) cc_final: 0.7628 (m-30) REVERT: A 197 PHE cc_start: 0.8447 (m-80) cc_final: 0.8177 (m-80) REVERT: A 364 ILE cc_start: 0.8741 (mp) cc_final: 0.8450 (tp) REVERT: A 436 MET cc_start: 0.9344 (mmp) cc_final: 0.9078 (mmm) REVERT: A 765 THR cc_start: 0.8805 (m) cc_final: 0.8586 (m) REVERT: A 766 PHE cc_start: 0.8416 (m-80) cc_final: 0.8195 (m-80) REVERT: A 785 ARG cc_start: 0.8285 (ttm110) cc_final: 0.7772 (ttt180) REVERT: A 900 PHE cc_start: 0.9151 (t80) cc_final: 0.8676 (t80) REVERT: A 1006 ARG cc_start: 0.7552 (ttt90) cc_final: 0.7160 (ttt90) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1865 time to fit residues: 58.4339 Evaluate side-chains 190 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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: 3.9990 chunk 63 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 51 optimal weight: 30.0000 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS A 566 GLN A 878 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9214 Z= 0.168 Angle : 0.584 8.204 12461 Z= 0.304 Chirality : 0.040 0.162 1426 Planarity : 0.004 0.071 1586 Dihedral : 10.516 99.311 1289 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1153 helix: 1.28 (0.20), residues: 709 sheet: 0.35 (0.85), residues: 35 loop : -2.02 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 704 HIS 0.003 0.001 HIS A 162 PHE 0.017 0.002 PHE A 78 TYR 0.043 0.002 TYR A 114 ARG 0.007 0.000 ARG A 485 *********************** 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 226 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.8754 (tp) cc_final: 0.8401 (tp) REVERT: A 174 ASP cc_start: 0.7842 (m-30) cc_final: 0.7513 (m-30) REVERT: A 436 MET cc_start: 0.9302 (mmp) cc_final: 0.9052 (mmm) REVERT: A 485 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7728 (mtm110) REVERT: A 765 THR cc_start: 0.8734 (m) cc_final: 0.8531 (m) REVERT: A 785 ARG cc_start: 0.8351 (ttm110) cc_final: 0.7650 (ttm170) REVERT: A 814 LEU cc_start: 0.8803 (mm) cc_final: 0.8407 (mt) REVERT: A 871 GLU cc_start: 0.8174 (tt0) cc_final: 0.7723 (tt0) REVERT: A 900 PHE cc_start: 0.9023 (t80) cc_final: 0.8413 (t80) REVERT: A 915 MET cc_start: 0.8051 (mpp) cc_final: 0.7331 (mpp) REVERT: A 937 THR cc_start: 0.9194 (t) cc_final: 0.8860 (t) REVERT: A 1003 HIS cc_start: 0.7713 (p-80) cc_final: 0.7496 (p-80) REVERT: A 1006 ARG cc_start: 0.7476 (ttt90) cc_final: 0.7120 (ttt90) REVERT: A 1207 GLU cc_start: 0.7423 (tp30) cc_final: 0.7157 (mp0) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1892 time to fit residues: 60.7015 Evaluate side-chains 197 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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: 0.8980 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 70 optimal weight: 0.0980 chunk 75 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS A 566 GLN A 878 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9214 Z= 0.163 Angle : 0.595 8.254 12461 Z= 0.307 Chirality : 0.041 0.352 1426 Planarity : 0.004 0.067 1586 Dihedral : 10.428 100.640 1289 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: 0.25 (0.25), residues: 1153 helix: 1.31 (0.19), residues: 713 sheet: 0.34 (0.84), residues: 35 loop : -2.02 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 704 HIS 0.003 0.001 HIS A1003 PHE 0.022 0.002 PHE A 767 TYR 0.015 0.001 TYR A1017 ARG 0.006 0.000 ARG A 485 *********************** 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 223 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASP cc_start: 0.7852 (m-30) cc_final: 0.7511 (m-30) REVERT: A 197 PHE cc_start: 0.8403 (m-80) cc_final: 0.8191 (m-80) REVERT: A 306 TYR cc_start: 0.8194 (t80) cc_final: 0.7954 (t80) REVERT: A 436 MET cc_start: 0.9292 (mmp) cc_final: 0.9037 (mmm) REVERT: A 485 ARG cc_start: 0.7900 (mtm110) cc_final: 0.7599 (mtm110) REVERT: A 765 THR cc_start: 0.8706 (m) cc_final: 0.8483 (m) REVERT: A 785 ARG cc_start: 0.8365 (ttm110) cc_final: 0.7595 (ttm110) REVERT: A 794 ARG cc_start: 0.8668 (mmm160) cc_final: 0.8291 (mmm160) REVERT: A 814 LEU cc_start: 0.8789 (mm) cc_final: 0.8394 (mt) REVERT: A 871 GLU cc_start: 0.8240 (tt0) cc_final: 0.7815 (tt0) REVERT: A 899 ASN cc_start: 0.9320 (m110) cc_final: 0.9087 (m110) REVERT: A 900 PHE cc_start: 0.9023 (t80) cc_final: 0.8375 (t80) REVERT: A 937 THR cc_start: 0.9233 (t) cc_final: 0.8906 (t) REVERT: A 1006 ARG cc_start: 0.7424 (ttt90) cc_final: 0.7053 (ttt90) REVERT: A 1207 GLU cc_start: 0.7434 (tp30) cc_final: 0.7228 (mp0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1985 time to fit residues: 63.3991 Evaluate side-chains 193 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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: 3.9990 chunk 106 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 0.0970 chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS A 566 GLN A 878 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9214 Z= 0.179 Angle : 0.592 8.304 12461 Z= 0.308 Chirality : 0.041 0.315 1426 Planarity : 0.004 0.066 1586 Dihedral : 10.413 100.252 1289 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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 (0.26), residues: 1153 helix: 1.36 (0.20), residues: 714 sheet: 0.32 (0.84), residues: 35 loop : -2.01 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 704 HIS 0.003 0.001 HIS A 394 PHE 0.022 0.002 PHE A 767 TYR 0.016 0.001 TYR A1017 ARG 0.006 0.000 ARG A 485 *********************** 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 220 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASP cc_start: 0.7811 (m-30) cc_final: 0.7509 (m-30) REVERT: A 197 PHE cc_start: 0.8380 (m-80) cc_final: 0.8140 (m-80) REVERT: A 306 TYR cc_start: 0.8325 (t80) cc_final: 0.7833 (t80) REVERT: A 436 MET cc_start: 0.9291 (mmp) cc_final: 0.9035 (mmm) REVERT: A 765 THR cc_start: 0.8660 (m) cc_final: 0.8443 (m) REVERT: A 785 ARG cc_start: 0.8455 (ttm110) cc_final: 0.7660 (ttm110) REVERT: A 794 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8240 (mmm160) REVERT: A 813 ARG cc_start: 0.7821 (tpt170) cc_final: 0.7348 (ttm170) REVERT: A 814 LEU cc_start: 0.8820 (mm) cc_final: 0.8391 (mt) REVERT: A 871 GLU cc_start: 0.8292 (tt0) cc_final: 0.7862 (tt0) REVERT: A 900 PHE cc_start: 0.9051 (t80) cc_final: 0.8456 (t80) REVERT: A 912 PHE cc_start: 0.8093 (m-10) cc_final: 0.7580 (m-80) REVERT: A 915 MET cc_start: 0.8047 (mpp) cc_final: 0.7055 (mpp) REVERT: A 937 THR cc_start: 0.9253 (t) cc_final: 0.8943 (t) REVERT: A 1006 ARG cc_start: 0.7468 (ttt90) cc_final: 0.7062 (ttt90) REVERT: A 1207 GLU cc_start: 0.7459 (tp30) cc_final: 0.7235 (mp0) REVERT: A 1211 GLN cc_start: 0.8782 (pp30) cc_final: 0.8496 (pp30) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1849 time to fit residues: 57.5659 Evaluate side-chains 190 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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: 1.9990 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 40.0000 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS A 566 GLN ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 0.029 9214 Z= 0.229 Angle : 0.625 8.297 12461 Z= 0.334 Chirality : 0.042 0.309 1426 Planarity : 0.004 0.063 1586 Dihedral : 10.585 98.942 1289 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.14 (0.25), residues: 1153 helix: 1.22 (0.20), residues: 712 sheet: 0.27 (0.84), residues: 35 loop : -2.04 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 704 HIS 0.003 0.001 HIS A 394 PHE 0.033 0.002 PHE A 953 TYR 0.019 0.002 TYR A1017 ARG 0.009 0.000 ARG A 485 ********************** 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 221 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 ASP cc_start: 0.7939 (m-30) cc_final: 0.7618 (m-30) REVERT: A 197 PHE cc_start: 0.8350 (m-80) cc_final: 0.8089 (m-10) REVERT: A 263 PHE cc_start: 0.8414 (m-80) cc_final: 0.7976 (m-80) REVERT: A 306 TYR cc_start: 0.8362 (t80) cc_final: 0.7701 (t80) REVERT: A 374 PHE cc_start: 0.8186 (m-80) cc_final: 0.7669 (t80) REVERT: A 436 MET cc_start: 0.9280 (mmp) cc_final: 0.9027 (mmm) REVERT: A 485 ARG cc_start: 0.7985 (mtm110) cc_final: 0.7719 (mtm110) REVERT: A 785 ARG cc_start: 0.8520 (ttm110) cc_final: 0.7789 (ttm170) REVERT: A 814 LEU cc_start: 0.8932 (mm) cc_final: 0.8608 (mt) REVERT: A 871 GLU cc_start: 0.8327 (tt0) cc_final: 0.7839 (tt0) REVERT: A 900 PHE cc_start: 0.9034 (t80) cc_final: 0.8496 (t80) REVERT: A 937 THR cc_start: 0.9287 (t) cc_final: 0.8973 (t) REVERT: A 1006 ARG cc_start: 0.7486 (ttt90) cc_final: 0.7071 (ttt90) REVERT: A 1207 GLU cc_start: 0.7446 (tp30) cc_final: 0.7215 (mp0) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1829 time to fit residues: 57.7072 Evaluate side-chains 191 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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: 0.9980 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 0.0170 chunk 5 optimal weight: 3.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS ** A 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 GLN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.165498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122615 restraints weight = 19090.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.126151 restraints weight = 13057.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.128861 restraints weight = 9834.158| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9214 Z= 0.243 Angle : 0.644 8.390 12461 Z= 0.345 Chirality : 0.043 0.312 1426 Planarity : 0.004 0.062 1586 Dihedral : 10.722 98.289 1289 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.01 (0.26), residues: 1153 helix: 1.10 (0.20), residues: 713 sheet: 0.22 (0.85), residues: 35 loop : -2.03 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 704 HIS 0.004 0.001 HIS A 394 PHE 0.022 0.002 PHE A 767 TYR 0.022 0.002 TYR A1017 ARG 0.008 0.000 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2050.20 seconds wall clock time: 37 minutes 31.72 seconds (2251.72 seconds total)