Starting phenix.real_space_refine on Fri Dec 8 20:00:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/12_2023/7zkb_14761_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/12_2023/7zkb_14761.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/12_2023/7zkb_14761_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/12_2023/7zkb_14761_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/12_2023/7zkb_14761_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/12_2023/7zkb_14761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/12_2023/7zkb_14761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/12_2023/7zkb_14761_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zkb_14761/12_2023/7zkb_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.96, per 1000 atoms: 0.55 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: 4.10 Conformation dependent library (CDL) restraints added in 1.7 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: 2.64 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: 2.83 Time building geometry restraints manager: 4.36 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=" C13 JJI A1402 " pdb=" N06 JJI A1402 " ideal model delta sigma weight residual 1.794 1.366 0.428 2.00e-02 2.50e+03 4.57e+02 bond pdb=" C08 JJI A1402 " pdb=" N04 JJI A1402 " ideal model delta sigma weight residual 1.786 1.364 0.422 2.00e-02 2.50e+03 4.44e+02 bond pdb=" C03 JJI A1402 " pdb=" N02 JJI A1402 " ideal model delta sigma weight residual 1.788 1.373 0.415 2.00e-02 2.50e+03 4.30e+02 bond pdb=" N4 JJI A1402 " pdb=" O41 JJI A1402 " ideal model delta sigma weight residual 1.176 1.404 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" N2 JJI A1402 " pdb=" O21 JJI A1402 " ideal model delta sigma weight residual 1.178 1.404 -0.226 2.00e-02 2.50e+03 1.27e+02 ... (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=" 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 angle pdb=" C ARG A 272 " pdb=" N TYR A 273 " pdb=" CA TYR A 273 " ideal model delta sigma weight residual 120.28 112.65 7.63 1.34e+00 5.57e-01 3.24e+01 ... (remaining 12456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 5361 35.45 - 70.90: 101 70.90 - 106.35: 17 106.35 - 141.80: 6 141.80 - 177.24: 2 Dihedral angle restraints: 5487 sinusoidal: 2176 harmonic: 3311 Sorted by residual: dihedral pdb=" C02 JJI A1402 " pdb=" C01 JJI A1402 " pdb=" N01 JJI A1402 " pdb=" C15 JJI A1402 " ideal model delta sinusoidal sigma weight residual 37.47 -145.29 -177.24 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C14 JJI A1402 " pdb=" C13 JJI A1402 " pdb=" C15 JJI A1402 " pdb=" N01 JJI A1402 " ideal model delta sinusoidal sigma weight residual -20.01 134.53 -154.54 1 3.00e+01 1.11e-03 2.03e+01 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 ... (remaining 5484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1187 0.071 - 0.143: 185 0.143 - 0.214: 39 0.214 - 0.286: 9 0.286 - 0.357: 6 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.940 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.060 Find NCS groups from input model: 0.250 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.540 ------------------------------------------------------------------------------- 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 : 0.011 0.428 9214 Z= 0.593 Angle : 1.059 17.364 12461 Z= 0.645 Chirality : 0.061 0.357 1426 Planarity : 0.005 0.062 1586 Dihedral : 15.650 177.244 3365 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 : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 246 average time/residue: 0.1945 time to fit residues: 68.0578 Evaluate side-chains 205 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.020 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0905 time to fit residues: 1.6058 ------------------------------------------------------------------------------- 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 154 GLN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** A1103 GLN A1253 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9214 Z= 0.183 Angle : 0.608 7.853 12461 Z= 0.312 Chirality : 0.041 0.209 1426 Planarity : 0.004 0.067 1586 Dihedral : 13.534 177.077 1284 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.11 % Allowed : 3.06 % 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: 0.10 (0.26), residues: 1153 helix: 1.12 (0.20), residues: 720 sheet: 0.23 (0.84), residues: 36 loop : -1.94 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 704 HIS 0.003 0.001 HIS A 241 PHE 0.031 0.002 PHE A 755 TYR 0.017 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 238 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1969 time to fit residues: 66.4938 Evaluate side-chains 194 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.907 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2563 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.0040 chunk 104 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 overall best weight: 1.3598 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9214 Z= 0.186 Angle : 0.594 7.930 12461 Z= 0.306 Chirality : 0.041 0.180 1426 Planarity : 0.004 0.050 1586 Dihedral : 12.911 174.419 1284 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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: 0.18 (0.26), residues: 1153 helix: 1.21 (0.20), residues: 717 sheet: 0.10 (0.84), residues: 36 loop : -1.93 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 704 HIS 0.003 0.001 HIS A 141 PHE 0.020 0.002 PHE A 196 TYR 0.016 0.001 TYR A 114 ARG 0.007 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 224 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1929 time to fit residues: 62.3495 Evaluate side-chains 196 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.033 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4989 ------------------------------------------------------------------------------- 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: 2.9990 chunk 54 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 0.0670 chunk 111 optimal weight: 7.9990 chunk 99 optimal weight: 0.0040 chunk 29 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 1.3534 ------------------------------------------------------------------------------- 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 A 899 ASN ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9214 Z= 0.189 Angle : 0.587 8.628 12461 Z= 0.304 Chirality : 0.041 0.273 1426 Planarity : 0.004 0.045 1586 Dihedral : 12.544 173.788 1284 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: 0.21 (0.26), residues: 1153 helix: 1.23 (0.20), residues: 718 sheet: 0.20 (0.84), residues: 36 loop : -1.95 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 704 HIS 0.002 0.001 HIS A 141 PHE 0.018 0.002 PHE A 196 TYR 0.015 0.001 TYR A 306 ARG 0.004 0.000 ARG A1188 *********************** 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 223 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2095 time to fit residues: 66.4649 Evaluate side-chains 189 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.0970 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 37 optimal weight: 20.0000 overall best weight: 1.7380 ------------------------------------------------------------------------------- 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 566 GLN ** A 834 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9214 Z= 0.214 Angle : 0.613 7.744 12461 Z= 0.316 Chirality : 0.041 0.211 1426 Planarity : 0.004 0.058 1586 Dihedral : 12.349 175.526 1284 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: 0.16 (0.26), residues: 1153 helix: 1.24 (0.20), residues: 710 sheet: 0.42 (0.85), residues: 35 loop : -2.03 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 704 HIS 0.002 0.001 HIS A 141 PHE 0.020 0.002 PHE A 147 TYR 0.016 0.001 TYR A 306 ARG 0.008 0.000 ARG A 785 *********************** 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 222 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1929 time to fit residues: 60.9554 Evaluate side-chains 191 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.032 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3912 ------------------------------------------------------------------------------- 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: 0.9990 chunk 27 optimal weight: 0.8980 chunk 111 optimal weight: 40.0000 chunk 92 optimal weight: 0.0970 chunk 51 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 878 GLN A1020 GLN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2191 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= 0.187 Angle : 0.608 8.053 12461 Z= 0.313 Chirality : 0.041 0.203 1426 Planarity : 0.004 0.065 1586 Dihedral : 12.001 174.938 1284 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.11 % Allowed : 1.58 % Favored : 98.31 % 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: 0.29 (0.26), residues: 1153 helix: 1.36 (0.20), residues: 711 sheet: 0.32 (0.83), residues: 35 loop : -2.02 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 704 HIS 0.002 0.001 HIS A1003 PHE 0.024 0.002 PHE A 766 TYR 0.016 0.001 TYR A1017 ARG 0.007 0.000 ARG A 485 *********************** 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 221 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 221 average time/residue: 0.1936 time to fit residues: 61.1428 Evaluate side-chains 191 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3998 ------------------------------------------------------------------------------- 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: 5.9990 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN A 795 GLN A 878 GLN A 899 ASN ** A1020 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2367 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= 0.186 Angle : 0.608 8.050 12461 Z= 0.315 Chirality : 0.041 0.195 1426 Planarity : 0.004 0.069 1586 Dihedral : 11.802 177.175 1284 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: 1.33 (0.20), residues: 717 sheet: 0.35 (0.84), residues: 35 loop : -2.06 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 158 HIS 0.002 0.001 HIS A 141 PHE 0.023 0.002 PHE A 767 TYR 0.016 0.001 TYR A1017 ARG 0.009 0.000 ARG A 785 *********************** 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 221 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1990 time to fit residues: 62.7122 Evaluate side-chains 190 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.028 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4135 ------------------------------------------------------------------------------- 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: 4.9990 chunk 21 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 0.0170 chunk 54 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 overall best weight: 3.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 276 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 HIS A 566 GLN A 834 GLN A 878 GLN A 932 HIS ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9214 Z= 0.317 Angle : 0.726 9.065 12461 Z= 0.388 Chirality : 0.045 0.363 1426 Planarity : 0.005 0.060 1586 Dihedral : 12.168 168.521 1284 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.41 (0.25), residues: 1153 helix: 0.66 (0.19), residues: 718 sheet: 0.05 (0.83), residues: 35 loop : -2.03 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 704 HIS 0.004 0.001 HIS A 241 PHE 0.036 0.003 PHE A 71 TYR 0.032 0.003 TYR A 114 ARG 0.013 0.001 ARG A 785 *********************** 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 212 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1945 time to fit residues: 59.1756 Evaluate side-chains 182 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4165 ------------------------------------------------------------------------------- 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: 9.9990 chunk 106 optimal weight: 7.9990 chunk 62 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 67 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 834 GLN A 878 GLN ** A1020 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9214 Z= 0.173 Angle : 0.642 8.287 12461 Z= 0.331 Chirality : 0.042 0.299 1426 Planarity : 0.004 0.068 1586 Dihedral : 11.690 170.010 1284 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: 0.12 (0.26), residues: 1153 helix: 1.21 (0.20), residues: 707 sheet: 0.24 (0.85), residues: 35 loop : -2.01 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 694 HIS 0.004 0.001 HIS A1003 PHE 0.028 0.002 PHE A 331 TYR 0.014 0.002 TYR A 946 ARG 0.008 0.001 ARG A 785 *********************** 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 221 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1984 time to fit residues: 62.6399 Evaluate side-chains 193 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2776 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 114 optimal weight: 40.0000 chunk 105 optimal weight: 0.0980 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN 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 A 899 ASN A 932 HIS ** A1020 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9214 Z= 0.191 Angle : 0.642 8.328 12461 Z= 0.332 Chirality : 0.043 0.305 1426 Planarity : 0.004 0.066 1586 Dihedral : 11.590 172.943 1284 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.11 % Allowed : 0.53 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.25), residues: 1153 helix: 1.13 (0.20), residues: 710 sheet: 0.27 (0.85), residues: 35 loop : -2.05 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 158 HIS 0.002 0.001 HIS A1003 PHE 0.024 0.002 PHE A 953 TYR 0.024 0.002 TYR A 113 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 214 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 213 time to evaluate : 1.094 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: 214 average time/residue: 0.1904 time to fit residues: 59.3439 Evaluate side-chains 184 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5066 ------------------------------------------------------------------------------- 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: 0.5980 chunk 84 optimal weight: 0.7980 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: 3.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 0.0010 chunk 5 optimal weight: 0.0060 overall best weight: 0.8804 ------------------------------------------------------------------------------- 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 ** 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** ** 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 = 0.4074 r_free = 0.4074 target = 0.172350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.128864 restraints weight = 19895.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.132741 restraints weight = 14278.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.134870 restraints weight = 9515.107| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9214 Z= 0.175 Angle : 0.639 8.380 12461 Z= 0.329 Chirality : 0.043 0.290 1426 Planarity : 0.004 0.066 1586 Dihedral : 11.372 177.057 1284 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % 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: 0.12 (0.26), residues: 1153 helix: 1.21 (0.20), residues: 710 sheet: 0.29 (0.85), residues: 35 loop : -2.04 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 704 HIS 0.006 0.001 HIS A 162 PHE 0.022 0.002 PHE A 767 TYR 0.027 0.002 TYR A 113 ARG 0.009 0.000 ARG A 485 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.89 seconds wall clock time: 38 minutes 59.06 seconds (2339.06 seconds total)