Starting phenix.real_space_refine on Sat Jul 20 12:03:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t77_41086/07_2024/8t77_41086.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t77_41086/07_2024/8t77_41086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t77_41086/07_2024/8t77_41086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t77_41086/07_2024/8t77_41086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t77_41086/07_2024/8t77_41086.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t77_41086/07_2024/8t77_41086.cif" } resolution = 3.25 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= 0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 114 5.49 5 S 16 5.16 5 C 6427 2.51 5 N 1889 2.21 5 O 2299 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 966": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 988": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1108": "OE1" <-> "OE2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A PHE 1276": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10745 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8328 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 27, 'TRANS': 997} Chain breaks: 8 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "B" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1905 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 78} Chain: "C" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 327 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 8.01, per 1000 atoms: 0.75 Number of scatterers: 10745 At special positions: 0 Unit cell: (85.8196, 120.814, 122.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 114 15.00 O 2299 8.00 N 1889 7.00 C 6427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.42 Conformation dependent library (CDL) restraints added in 1.6 seconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 5 sheets defined 55.7% alpha, 7.3% beta 35 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.650A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.828A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 181 through 196 Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 343 through 353 removed outlier: 3.585A pdb=" N TYR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix removed outlier: 3.568A pdb=" N MET A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.187A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.192A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.597A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.615A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.999A pdb=" N ARG A 494 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.274A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 609 removed outlier: 3.743A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 4.135A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.526A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 650 removed outlier: 3.603A pdb=" N LYS A 649 " --> pdb=" O ASP A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.701A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 710 removed outlier: 4.151A pdb=" N GLN A 709 " --> pdb=" O LYS A 705 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 4.008A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.893A pdb=" N LYS A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE A 737 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.663A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.738A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 999 removed outlier: 4.776A pdb=" N ALA A 987 " --> pdb=" O HIS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.501A pdb=" N ARG A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 removed outlier: 3.819A pdb=" N ILE A1195 " --> pdb=" O LYS A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 removed outlier: 3.831A pdb=" N SER A1240 " --> pdb=" O LEU A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1246 Processing helix chain 'A' and resid 1251 through 1261 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 3.676A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1297 Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1313 through 1315 No H-bonds generated for 'chain 'A' and resid 1313 through 1315' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.655A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY A 8 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 49 " --> pdb=" O TRP A 18 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A 48 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL A1095 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA A 50 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 10.174A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.924A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1325 360 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 4.57 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2297 1.33 - 1.45: 2911 1.45 - 1.57: 5718 1.57 - 1.69: 226 1.69 - 1.81: 30 Bond restraints: 11182 Sorted by residual: bond pdb=" CB ASP A 406 " pdb=" CG ASP A 406 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.50e-02 1.60e+03 3.93e+00 bond pdb=" CB GLN A1091 " pdb=" CG GLN A1091 " ideal model delta sigma weight residual 1.520 1.575 -0.055 3.00e-02 1.11e+03 3.37e+00 bond pdb=" CB ASP A 384 " pdb=" CG ASP A 384 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.82e+00 bond pdb=" CB GLU A 470 " pdb=" CG GLU A 470 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CG GLN A1091 " pdb=" CD GLN A1091 " ideal model delta sigma weight residual 1.516 1.554 -0.038 2.50e-02 1.60e+03 2.29e+00 ... (remaining 11177 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.22: 604 105.22 - 112.46: 5753 112.46 - 119.70: 4123 119.70 - 126.94: 4755 126.94 - 134.18: 365 Bond angle restraints: 15600 Sorted by residual: angle pdb=" CA LEU A 651 " pdb=" CB LEU A 651 " pdb=" CG LEU A 651 " ideal model delta sigma weight residual 116.30 132.31 -16.01 3.50e+00 8.16e-02 2.09e+01 angle pdb=" CA LEU A1282 " pdb=" CB LEU A1282 " pdb=" CG LEU A1282 " ideal model delta sigma weight residual 116.30 132.29 -15.99 3.50e+00 8.16e-02 2.09e+01 angle pdb=" CB GLN A1091 " pdb=" CG GLN A1091 " pdb=" CD GLN A1091 " ideal model delta sigma weight residual 112.60 119.66 -7.06 1.70e+00 3.46e-01 1.72e+01 angle pdb=" CB LYS A 999 " pdb=" CG LYS A 999 " pdb=" CD LYS A 999 " ideal model delta sigma weight residual 111.30 120.61 -9.31 2.30e+00 1.89e-01 1.64e+01 angle pdb=" CA LYS A 999 " pdb=" CB LYS A 999 " pdb=" CG LYS A 999 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 ... (remaining 15595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.44: 6266 30.44 - 60.88: 452 60.88 - 91.32: 79 91.32 - 121.77: 3 121.77 - 152.21: 2 Dihedral angle restraints: 6802 sinusoidal: 3786 harmonic: 3016 Sorted by residual: dihedral pdb=" CA TRP A 464 " pdb=" C TRP A 464 " pdb=" N MET A 465 " pdb=" CA MET A 465 " ideal model delta harmonic sigma weight residual -180.00 -153.34 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA LYS A1107 " pdb=" C LYS A1107 " pdb=" N GLU A1108 " pdb=" CA GLU A1108 " ideal model delta harmonic sigma weight residual 180.00 -153.45 -26.55 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA VAL A1259 " pdb=" C VAL A1259 " pdb=" N GLU A1260 " pdb=" CA GLU A1260 " ideal model delta harmonic sigma weight residual 180.00 153.61 26.39 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 6799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1591 0.078 - 0.155: 206 0.155 - 0.233: 16 0.233 - 0.310: 3 0.310 - 0.388: 4 Chirality restraints: 1820 Sorted by residual: chirality pdb=" CB ILE A1352 " pdb=" CA ILE A1352 " pdb=" CG1 ILE A1352 " pdb=" CG2 ILE A1352 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.77e+00 chirality pdb=" CG LEU A 597 " pdb=" CB LEU A 597 " pdb=" CD1 LEU A 597 " pdb=" CD2 LEU A 597 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C1' DC D 44 " pdb=" O4' DC D 44 " pdb=" C2' DC D 44 " pdb=" N1 DC D 44 " both_signs ideal model delta sigma weight residual False 2.47 2.15 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1817 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 19 " -0.022 2.00e-02 2.50e+03 2.40e-02 1.73e+01 pdb=" N9 G B 19 " 0.059 2.00e-02 2.50e+03 pdb=" C8 G B 19 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G B 19 " -0.011 2.00e-02 2.50e+03 pdb=" C5 G B 19 " 0.010 2.00e-02 2.50e+03 pdb=" C6 G B 19 " 0.022 2.00e-02 2.50e+03 pdb=" O6 G B 19 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 19 " -0.014 2.00e-02 2.50e+03 pdb=" C2 G B 19 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G B 19 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G B 19 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 19 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1276 " 0.024 2.00e-02 2.50e+03 2.96e-02 1.53e+01 pdb=" CG PHE A1276 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A1276 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A1276 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE A1276 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A1276 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A1276 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 517 " 0.023 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR A 517 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 517 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR A 517 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 517 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 517 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 517 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 517 " -0.007 2.00e-02 2.50e+03 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 442 2.70 - 3.25: 10213 3.25 - 3.80: 18734 3.80 - 4.35: 23697 4.35 - 4.90: 35637 Nonbonded interactions: 88723 Sorted by model distance: nonbonded pdb=" O GLY A 736 " pdb=" OG1 THR A 740 " model vdw 2.153 2.440 nonbonded pdb=" OD1 ASP A1267 " pdb=" OH TYR A1294 " model vdw 2.245 2.440 nonbonded pdb=" O LEU A 455 " pdb=" O2' G B 58 " model vdw 2.256 2.440 nonbonded pdb=" OG1 THR A1102 " pdb=" OP2 U B 64 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.295 2.440 ... (remaining 88718 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 37.210 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.005 0.055 11182 Z= 0.290 Angle : 0.990 16.010 15600 Z= 0.509 Chirality : 0.054 0.388 1820 Planarity : 0.007 0.082 1561 Dihedral : 19.381 152.208 4842 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.78 % Allowed : 21.18 % Favored : 78.05 % 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: -1.56 (0.24), residues: 1008 helix: -1.21 (0.20), residues: 502 sheet: -0.24 (0.51), residues: 110 loop : -0.76 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.005 TRP A 18 HIS 0.015 0.002 HIS A 137 PHE 0.068 0.003 PHE A1276 TYR 0.068 0.004 TYR A 517 ARG 0.021 0.001 ARG A1111 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 GLN cc_start: 0.9085 (mt0) cc_final: 0.8484 (mm-40) REVERT: A 397 ASP cc_start: 0.7808 (t0) cc_final: 0.7533 (t0) REVERT: A 482 VAL cc_start: 0.9068 (t) cc_final: 0.8757 (p) outliers start: 7 outliers final: 2 residues processed: 87 average time/residue: 0.2564 time to fit residues: 31.5906 Evaluate side-chains 76 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 1095 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 459 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 511 HIS A 612 ASN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 HIS ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1335 GLN A1349 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11182 Z= 0.334 Angle : 0.689 9.894 15600 Z= 0.363 Chirality : 0.041 0.194 1820 Planarity : 0.005 0.044 1561 Dihedral : 19.977 153.513 2729 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.22 % Allowed : 18.85 % Favored : 77.94 % 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: -0.75 (0.25), residues: 1008 helix: -0.21 (0.22), residues: 522 sheet: -0.61 (0.53), residues: 101 loop : -0.64 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 18 HIS 0.008 0.002 HIS A 137 PHE 0.019 0.002 PHE A 966 TYR 0.029 0.002 TYR A 450 ARG 0.007 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 76 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8448 (t0) cc_final: 0.8222 (t0) REVERT: A 495 MET cc_start: 0.7576 (mmm) cc_final: 0.7352 (mmp) REVERT: A 692 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8986 (p0) REVERT: A 961 LYS cc_start: 0.9276 (mttt) cc_final: 0.9045 (mppt) REVERT: A 1099 GLU cc_start: 0.8673 (pm20) cc_final: 0.8424 (pm20) REVERT: A 1208 ASN cc_start: 0.9242 (t0) cc_final: 0.8946 (t0) outliers start: 29 outliers final: 21 residues processed: 97 average time/residue: 0.2215 time to fit residues: 31.3240 Evaluate side-chains 84 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1170 GLU Chi-restraints excluded: chain A residue 1172 SER Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 11182 Z= 0.361 Angle : 0.672 10.123 15600 Z= 0.358 Chirality : 0.041 0.201 1820 Planarity : 0.004 0.039 1561 Dihedral : 20.008 153.351 2727 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.54 % Allowed : 18.29 % Favored : 76.16 % 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: -0.62 (0.25), residues: 1008 helix: 0.04 (0.22), residues: 525 sheet: -0.41 (0.55), residues: 97 loop : -0.87 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1136 HIS 0.008 0.001 HIS A 328 PHE 0.018 0.002 PHE A 98 TYR 0.024 0.002 TYR A 450 ARG 0.007 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 71 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.9050 (tptp) cc_final: 0.8752 (tptp) REVERT: A 657 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.7999 (m) REVERT: A 734 LYS cc_start: 0.8431 (mttt) cc_final: 0.8074 (mttt) REVERT: A 961 LYS cc_start: 0.9299 (mttt) cc_final: 0.9056 (mppt) REVERT: A 1108 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: A 1208 ASN cc_start: 0.9097 (t0) cc_final: 0.8646 (t0) REVERT: A 1276 PHE cc_start: 0.8900 (t80) cc_final: 0.8615 (t80) outliers start: 50 outliers final: 29 residues processed: 113 average time/residue: 0.2378 time to fit residues: 38.6897 Evaluate side-chains 89 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 58 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 20.0000 chunk 67 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 0.0170 overall best weight: 1.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11182 Z= 0.206 Angle : 0.552 10.432 15600 Z= 0.291 Chirality : 0.037 0.196 1820 Planarity : 0.004 0.038 1561 Dihedral : 19.885 150.816 2727 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.88 % Allowed : 18.07 % Favored : 77.05 % 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: -0.24 (0.26), residues: 1008 helix: 0.45 (0.23), residues: 517 sheet: -0.27 (0.55), residues: 97 loop : -0.81 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.016 0.002 PHE A 970 TYR 0.026 0.002 TYR A 988 ARG 0.003 0.000 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 69 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 PHE cc_start: 0.5109 (p90) cc_final: 0.4588 (p90) REVERT: A 397 ASP cc_start: 0.8716 (t0) cc_final: 0.8500 (t0) REVERT: A 492 ILE cc_start: 0.9573 (OUTLIER) cc_final: 0.9347 (pt) REVERT: A 601 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8736 (tt) REVERT: A 734 LYS cc_start: 0.8464 (mttt) cc_final: 0.8000 (mttt) REVERT: A 961 LYS cc_start: 0.9277 (mttt) cc_final: 0.8992 (mppt) REVERT: A 1208 ASN cc_start: 0.9092 (t0) cc_final: 0.8624 (t0) REVERT: A 1287 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8545 (mm) outliers start: 44 outliers final: 24 residues processed: 98 average time/residue: 0.2320 time to fit residues: 32.9084 Evaluate side-chains 87 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 60 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 601 ILE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11182 Z= 0.332 Angle : 0.638 9.713 15600 Z= 0.336 Chirality : 0.040 0.202 1820 Planarity : 0.004 0.036 1561 Dihedral : 19.917 153.461 2727 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.99 % Allowed : 19.07 % Favored : 76.94 % 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: -0.33 (0.26), residues: 1008 helix: 0.35 (0.23), residues: 511 sheet: -0.23 (0.57), residues: 92 loop : -0.83 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1136 HIS 0.008 0.002 HIS A 328 PHE 0.025 0.002 PHE A 693 TYR 0.022 0.002 TYR A 136 ARG 0.005 0.001 ARG A 654 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 66 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 397 ASP cc_start: 0.8779 (t0) cc_final: 0.8496 (t0) REVERT: A 492 ILE cc_start: 0.9606 (OUTLIER) cc_final: 0.9379 (pt) REVERT: A 734 LYS cc_start: 0.8715 (mttt) cc_final: 0.8280 (mttt) REVERT: A 961 LYS cc_start: 0.9293 (mttt) cc_final: 0.9011 (mppt) REVERT: A 1287 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8650 (mt) outliers start: 36 outliers final: 25 residues processed: 95 average time/residue: 0.2411 time to fit residues: 32.6773 Evaluate side-chains 83 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 56 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11182 Z= 0.281 Angle : 0.588 9.710 15600 Z= 0.311 Chirality : 0.038 0.189 1820 Planarity : 0.004 0.039 1561 Dihedral : 19.774 151.987 2727 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.10 % Allowed : 19.18 % Favored : 76.72 % 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: -0.33 (0.26), residues: 1008 helix: 0.45 (0.23), residues: 514 sheet: -0.13 (0.60), residues: 82 loop : -1.01 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.014 0.002 PHE A 98 TYR 0.024 0.002 TYR A 136 ARG 0.005 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 60 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ILE cc_start: 0.9607 (OUTLIER) cc_final: 0.9386 (pt) REVERT: A 629 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7194 (mmp-170) REVERT: A 734 LYS cc_start: 0.8799 (mttt) cc_final: 0.8366 (mttt) REVERT: A 961 LYS cc_start: 0.9305 (mttt) cc_final: 0.9023 (mppt) REVERT: A 1118 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8594 (mtpp) outliers start: 37 outliers final: 29 residues processed: 90 average time/residue: 0.2504 time to fit residues: 31.8779 Evaluate side-chains 88 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 56 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11182 Z= 0.319 Angle : 0.624 9.207 15600 Z= 0.331 Chirality : 0.040 0.203 1820 Planarity : 0.004 0.036 1561 Dihedral : 19.824 153.042 2727 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 4.88 % Allowed : 20.18 % Favored : 74.94 % 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: -0.55 (0.25), residues: 1008 helix: 0.32 (0.22), residues: 511 sheet: -0.27 (0.59), residues: 82 loop : -1.16 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1136 HIS 0.008 0.001 HIS A 328 PHE 0.014 0.002 PHE A 98 TYR 0.024 0.002 TYR A 136 ARG 0.004 0.001 ARG A 635 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 64 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ILE cc_start: 0.9617 (OUTLIER) cc_final: 0.9403 (pt) REVERT: A 627 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7861 (mm-30) REVERT: A 629 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7135 (mmp-170) REVERT: A 734 LYS cc_start: 0.8803 (mttt) cc_final: 0.8405 (mttt) REVERT: A 958 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8049 (tp) REVERT: A 961 LYS cc_start: 0.9309 (mttt) cc_final: 0.9020 (mppt) REVERT: A 1118 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8605 (mtpp) outliers start: 44 outliers final: 34 residues processed: 101 average time/residue: 0.2392 time to fit residues: 34.8154 Evaluate side-chains 96 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 58 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Chi-restraints excluded: chain A residue 1362 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 0.1980 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11182 Z= 0.254 Angle : 0.566 9.276 15600 Z= 0.302 Chirality : 0.038 0.195 1820 Planarity : 0.004 0.035 1561 Dihedral : 19.677 151.340 2727 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.43 % Allowed : 20.95 % Favored : 74.61 % 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: -0.37 (0.26), residues: 1008 helix: 0.54 (0.23), residues: 511 sheet: -0.30 (0.58), residues: 82 loop : -1.18 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1136 HIS 0.006 0.001 HIS A 328 PHE 0.025 0.001 PHE A 518 TYR 0.024 0.002 TYR A 136 ARG 0.003 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 65 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ILE cc_start: 0.9604 (OUTLIER) cc_final: 0.9387 (pt) REVERT: A 629 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7147 (mmp-170) REVERT: A 734 LYS cc_start: 0.8855 (mttt) cc_final: 0.8471 (mttt) REVERT: A 958 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8022 (tp) REVERT: A 961 LYS cc_start: 0.9299 (mttt) cc_final: 0.9008 (mppt) REVERT: A 1118 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8585 (mtpp) outliers start: 40 outliers final: 29 residues processed: 98 average time/residue: 0.2399 time to fit residues: 33.7414 Evaluate side-chains 94 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 61 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1118 LYS Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1254 GLN Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.0020 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 0.2980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11182 Z= 0.152 Angle : 0.519 9.242 15600 Z= 0.274 Chirality : 0.036 0.169 1820 Planarity : 0.003 0.033 1561 Dihedral : 19.369 148.433 2727 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.10 % Allowed : 22.95 % Favored : 73.95 % 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: -0.06 (0.26), residues: 1008 helix: 0.79 (0.23), residues: 517 sheet: -0.14 (0.65), residues: 69 loop : -1.01 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 476 HIS 0.004 0.001 HIS A 137 PHE 0.030 0.001 PHE A 518 TYR 0.021 0.001 TYR A 136 ARG 0.003 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 72 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ILE cc_start: 0.9587 (OUTLIER) cc_final: 0.9372 (pt) REVERT: A 495 MET cc_start: 0.7477 (mmm) cc_final: 0.7204 (mmp) REVERT: A 629 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.6897 (mmp80) REVERT: A 734 LYS cc_start: 0.8859 (mttt) cc_final: 0.8478 (mttt) REVERT: A 958 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7945 (tp) REVERT: A 961 LYS cc_start: 0.9286 (mttt) cc_final: 0.8981 (mppt) outliers start: 28 outliers final: 21 residues processed: 92 average time/residue: 0.2578 time to fit residues: 33.6208 Evaluate side-chains 88 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 64 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 93 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11182 Z= 0.191 Angle : 0.539 9.174 15600 Z= 0.285 Chirality : 0.036 0.168 1820 Planarity : 0.003 0.033 1561 Dihedral : 19.374 149.776 2727 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.77 % Allowed : 23.73 % Favored : 73.50 % 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: 1008 helix: 0.74 (0.23), residues: 517 sheet: -0.14 (0.65), residues: 69 loop : -1.02 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.025 0.001 PHE A 518 TYR 0.024 0.002 TYR A1326 ARG 0.002 0.000 ARG A 654 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 65 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 VAL cc_start: 0.8916 (t) cc_final: 0.8675 (p) REVERT: A 492 ILE cc_start: 0.9595 (OUTLIER) cc_final: 0.9393 (pt) REVERT: A 495 MET cc_start: 0.7524 (mmm) cc_final: 0.7263 (mmp) REVERT: A 629 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7031 (mmp80) REVERT: A 734 LYS cc_start: 0.8852 (mttt) cc_final: 0.8492 (mttt) REVERT: A 961 LYS cc_start: 0.9290 (mttt) cc_final: 0.8982 (mppt) REVERT: A 1099 GLU cc_start: 0.8362 (pm20) cc_final: 0.8109 (pm20) REVERT: A 1177 ASN cc_start: 0.8823 (t0) cc_final: 0.8523 (t0) outliers start: 25 outliers final: 22 residues processed: 83 average time/residue: 0.2898 time to fit residues: 34.0873 Evaluate side-chains 86 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 62 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 504 ASN Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 554 LYS Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 629 ARG Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1142 SER Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1287 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.085103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061952 restraints weight = 42981.656| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.19 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11182 Z= 0.188 Angle : 0.543 10.825 15600 Z= 0.285 Chirality : 0.036 0.170 1820 Planarity : 0.003 0.033 1561 Dihedral : 19.368 149.940 2727 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.88 % Allowed : 23.61 % Favored : 73.50 % 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: 1008 helix: 0.73 (0.23), residues: 517 sheet: -0.37 (0.63), residues: 74 loop : -0.99 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.023 0.001 PHE A 518 TYR 0.021 0.002 TYR A 136 ARG 0.002 0.000 ARG A1303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.06 seconds wall clock time: 41 minutes 20.52 seconds (2480.52 seconds total)