Starting phenix.real_space_refine on Thu Feb 15 09:16:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/02_2024/8d4a_27179.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/02_2024/8d4a_27179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/02_2024/8d4a_27179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/02_2024/8d4a_27179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/02_2024/8d4a_27179.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d4a_27179/02_2024/8d4a_27179.pdb" } resolution = 2.74 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= 0.019 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 90 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 7151 2.51 5 N 2026 2.21 5 O 2498 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 32": "OE1" <-> "OE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 448": "OE1" <-> "OE2" Residue "A GLU 550": "OE1" <-> "OE2" Residue "A GLU 560": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A ASP 601": "OD1" <-> "OD2" Residue "A TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A GLU 666": "OE1" <-> "OE2" Residue "A ASP 674": "OD1" <-> "OD2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 848": "OD1" <-> "OD2" Residue "A GLU 885": "OE1" <-> "OE2" Residue "A GLU 933": "OE1" <-> "OE2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A GLU 962": "OE1" <-> "OE2" Residue "A ASP 975": "OD1" <-> "OD2" Residue "A GLU 977": "OE1" <-> "OE2" Residue "A ARG 981": "NH1" <-> "NH2" Residue "A GLU 983": "OE1" <-> "OE2" Residue "A ARG 1004": "NH1" <-> "NH2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "A ARG 1016": "NH1" <-> "NH2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1079": "NH1" <-> "NH2" Residue "A GLU 1088": "OE1" <-> "OE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1140": "NH1" <-> "NH2" Residue "A ARG 1144": "NH1" <-> "NH2" Residue "A ASP 1196": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11798 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 9880 Classifications: {'peptide': 1207} Link IDs: {'PTRANS': 29, 'TRANS': 1177} Chain breaks: 2 Chain: "B" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 870 Classifications: {'RNA': 41} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 20, 'rna3p_pyr': 16} Link IDs: {'rna2p': 5, 'rna3p': 35} Chain: "C" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 593 Classifications: {'RNA': 28} Modifications used: {'rna2p_pur': 5, 'rna3p_pur': 8, 'rna3p_pyr': 15} Link IDs: {'rna2p': 4, 'rna3p': 23} Chain: "D" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 220 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "G" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3, 'water': 1} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9380 SG CYS A1170 55.459 39.309 111.834 1.00 28.74 S ATOM 9400 SG CYS A1173 56.581 41.503 114.636 1.00 30.25 S ATOM 9522 SG CYS A1188 58.987 38.971 113.049 1.00 36.82 S ATOM 9546 SG CYS A1191 56.134 37.742 115.244 1.00 40.43 S Time building chain proxies: 7.15, per 1000 atoms: 0.61 Number of scatterers: 11798 At special positions: 0 Unit cell: (115.62, 99.64, 125.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 30 16.00 P 90 15.00 Mg 2 11.99 O 2498 8.00 N 2026 7.00 C 7151 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: 5.21 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1301 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1170 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1188 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1173 " pdb="ZN ZN A1301 " - pdb=" SG CYS A1191 " Number of angles added : 6 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 10 sheets defined 55.5% alpha, 13.4% beta 28 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.648A pdb=" N THR A 6 " --> pdb=" O HIS A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 48 removed outlier: 3.797A pdb=" N SER A 48 " --> pdb=" O ASN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 79 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 128 through 163 removed outlier: 3.644A pdb=" N ILE A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 removed outlier: 3.991A pdb=" N ALA A 167 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N HIS A 168 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS A 170 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 removed outlier: 4.101A pdb=" N ILE A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.865A pdb=" N ILE A 204 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER A 205 " --> pdb=" O PRO A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 201 through 205' Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 239 removed outlier: 4.302A pdb=" N LEU A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 263 through 275 Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.599A pdb=" N LYS A 333 " --> pdb=" O HIS A 329 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N GLU A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 371 through 375 removed outlier: 3.514A pdb=" N TYR A 375 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 391 Processing helix chain 'A' and resid 399 through 412 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'A' and resid 418 through 438 Processing helix chain 'A' and resid 446 through 460 removed outlier: 4.455A pdb=" N PHE A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 Processing helix chain 'A' and resid 486 through 503 removed outlier: 3.510A pdb=" N GLY A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 557 removed outlier: 3.769A pdb=" N GLN A 539 " --> pdb=" O ASN A 535 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU A 557 " --> pdb=" O ASP A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 560 No H-bonds generated for 'chain 'A' and resid 558 through 560' Processing helix chain 'A' and resid 591 through 598 Processing helix chain 'A' and resid 615 through 625 removed outlier: 3.629A pdb=" N LYS A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 653 Processing helix chain 'A' and resid 654 through 659 Processing helix chain 'A' and resid 661 through 675 removed outlier: 3.728A pdb=" N SER A 675 " --> pdb=" O CYS A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 681 Processing helix chain 'A' and resid 682 through 687 Processing helix chain 'A' and resid 695 through 707 Processing helix chain 'A' and resid 716 through 726 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.747A pdb=" N PHE A 757 " --> pdb=" O TRP A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 808 through 818 removed outlier: 3.736A pdb=" N ASP A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 838 Processing helix chain 'A' and resid 882 through 886 removed outlier: 3.504A pdb=" N SER A 886 " --> pdb=" O ARG A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 922 No H-bonds generated for 'chain 'A' and resid 920 through 922' Processing helix chain 'A' and resid 940 through 961 removed outlier: 4.010A pdb=" N LYS A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 945 " --> pdb=" O GLN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 961 through 967 Processing helix chain 'A' and resid 968 through 970 No H-bonds generated for 'chain 'A' and resid 968 through 970' Processing helix chain 'A' and resid 974 through 983 Processing helix chain 'A' and resid 999 through 1016 Processing helix chain 'A' and resid 1019 through 1028 removed outlier: 3.693A pdb=" N ILE A1026 " --> pdb=" O GLU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1054 removed outlier: 3.681A pdb=" N ASN A1042 " --> pdb=" O GLY A1038 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N MET A1043 " --> pdb=" O ILE A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1100 Processing helix chain 'A' and resid 1105 through 1117 Processing helix chain 'A' and resid 1202 through 1209 removed outlier: 5.928A pdb=" N HIS A1207 " --> pdb=" O ASN A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1232 removed outlier: 3.708A pdb=" N SER A1224 " --> pdb=" O ILE A1220 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN A1230 " --> pdb=" O GLU A1226 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 18 removed outlier: 3.925A pdb=" N ALA A 770 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN A 796 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU A 768 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 769 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS A 248 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 771 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS A 566 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS A 248 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY A 568 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR A 250 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE A 570 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 715 removed outlier: 6.651A pdb=" N VAL A 611 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 9.965A pdb=" N GLY A 568 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 14.983A pdb=" N SER A 613 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 17.816A pdb=" N HIS A 566 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N HIS A 566 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LYS A 248 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY A 568 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N THR A 250 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE A 570 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 771 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS A 248 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A 769 " --> pdb=" O LYS A 248 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU A 768 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASN A 796 " --> pdb=" O GLU A 768 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA A 770 " --> pdb=" O ALA A 794 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 123 Processing sheet with id=AA5, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.372A pdb=" N VAL A 859 " --> pdb=" O LEU A 867 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 866 through 867 removed outlier: 4.372A pdb=" N VAL A 859 " --> pdb=" O LEU A 867 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU A1063 " --> pdb=" O ILE A 847 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ARG A 849 " --> pdb=" O GLU A1063 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 887 through 896 removed outlier: 6.782A pdb=" N ILE A 872 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR A 895 " --> pdb=" O PHE A 870 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N PHE A 870 " --> pdb=" O THR A 895 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N GLU A 871 " --> pdb=" O LYS A 914 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 916 " --> pdb=" O GLU A 871 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LYS A 875 " --> pdb=" O ASP A 918 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AA9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB1, first strand: chain 'A' and resid 1178 through 1180 520 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 6.54 Time building geometry restraints manager: 5.49 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: 2645 1.33 - 1.45: 2991 1.45 - 1.57: 6357 1.57 - 1.69: 177 1.69 - 1.81: 43 Bond restraints: 12213 Sorted by residual: bond pdb=" C3' DT D 5 " pdb=" O3' DT D 5 " ideal model delta sigma weight residual 1.422 1.474 -0.052 3.00e-02 1.11e+03 3.01e+00 bond pdb=" CG1 ILE A 81 " pdb=" CD1 ILE A 81 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.87e+00 bond pdb=" CG1 ILE A1161 " pdb=" CD1 ILE A1161 " ideal model delta sigma weight residual 1.513 1.460 0.053 3.90e-02 6.57e+02 1.86e+00 bond pdb=" CG LEU A 119 " pdb=" CD1 LEU A 119 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.85e+00 bond pdb=" C HIS A 374 " pdb=" N TYR A 375 " ideal model delta sigma weight residual 1.327 1.304 0.023 1.71e-02 3.42e+03 1.81e+00 ... (remaining 12208 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.38: 680 106.38 - 113.30: 6616 113.30 - 120.21: 4504 120.21 - 127.13: 4796 127.13 - 134.04: 278 Bond angle restraints: 16874 Sorted by residual: angle pdb=" C SER A1122 " pdb=" N ASP A1123 " pdb=" CA ASP A1123 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" O3' G B 41 " pdb=" C3' G B 41 " pdb=" C2' G B 41 " ideal model delta sigma weight residual 113.70 118.98 -5.28 1.50e+00 4.44e-01 1.24e+01 angle pdb=" N ASP A 869 " pdb=" CA ASP A 869 " pdb=" C ASP A 869 " ideal model delta sigma weight residual 110.44 106.45 3.99 1.20e+00 6.94e-01 1.11e+01 angle pdb=" C4' G B 41 " pdb=" C3' G B 41 " pdb=" O3' G B 41 " ideal model delta sigma weight residual 113.00 117.79 -4.79 1.50e+00 4.44e-01 1.02e+01 angle pdb=" C ILE A 81 " pdb=" CA ILE A 81 " pdb=" CB ILE A 81 " ideal model delta sigma weight residual 110.63 113.60 -2.97 9.40e-01 1.13e+00 1.00e+01 ... (remaining 16869 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 7110 35.27 - 70.54: 314 70.54 - 105.81: 21 105.81 - 141.08: 0 141.08 - 176.35: 3 Dihedral angle restraints: 7448 sinusoidal: 3880 harmonic: 3568 Sorted by residual: dihedral pdb=" O4' U B 14 " pdb=" C1' U B 14 " pdb=" N1 U B 14 " pdb=" C2 U B 14 " ideal model delta sinusoidal sigma weight residual 200.00 48.75 151.25 1 1.50e+01 4.44e-03 8.01e+01 dihedral pdb=" CA ILE A 734 " pdb=" C ILE A 734 " pdb=" N ASN A 735 " pdb=" CA ASN A 735 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA TYR A1139 " pdb=" C TYR A1139 " pdb=" N ARG A1140 " pdb=" CA ARG A1140 " ideal model delta harmonic sigma weight residual 180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 7445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1660 0.066 - 0.132: 218 0.132 - 0.199: 14 0.199 - 0.265: 1 0.265 - 0.331: 1 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C3' G B 41 " pdb=" C4' G B 41 " pdb=" O3' G B 41 " pdb=" C2' G B 41 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA ASN A1227 " pdb=" N ASN A1227 " pdb=" C ASN A1227 " pdb=" CB ASN A1227 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C1' U B 14 " pdb=" O4' U B 14 " pdb=" C2' U B 14 " pdb=" N1 U B 14 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 8.08e-01 ... (remaining 1891 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 337 " -0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO A 338 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 255 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.55e+00 pdb=" C THR A 255 " -0.037 2.00e-02 2.50e+03 pdb=" O THR A 255 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA A 256 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 170 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.72e+00 pdb=" N PRO A 171 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " 0.027 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 219 2.66 - 3.22: 10073 3.22 - 3.78: 19328 3.78 - 4.34: 28550 4.34 - 4.90: 43674 Nonbonded interactions: 101844 Sorted by model distance: nonbonded pdb=" OE2 GLU A1063 " pdb="MG MG A1302 " model vdw 2.098 2.170 nonbonded pdb=" OE1 GLU A1063 " pdb="MG MG A1302 " model vdw 2.106 2.170 nonbonded pdb=" OD1 ASP A 848 " pdb="MG MG A1302 " model vdw 2.130 2.170 nonbonded pdb=" O PHE A 218 " pdb=" OH TYR A 223 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR A 393 " pdb=" OD1 ASP A 426 " model vdw 2.260 2.440 ... (remaining 101839 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: 2.620 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: 11.990 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 43.450 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 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 : 0.006 0.053 12213 Z= 0.356 Angle : 0.713 10.044 16874 Z= 0.407 Chirality : 0.045 0.331 1894 Planarity : 0.004 0.066 1841 Dihedral : 17.649 176.354 5142 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.09 % Allowed : 0.00 % Favored : 99.91 % 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: -0.49 (0.22), residues: 1201 helix: -0.14 (0.19), residues: 603 sheet: -0.25 (0.40), residues: 155 loop : -0.35 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 480 HIS 0.005 0.001 HIS A 640 PHE 0.023 0.003 PHE A 757 TYR 0.019 0.002 TYR A1139 ARG 0.013 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.259 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 2.0312 time to fit residues: 238.5600 Evaluate side-chains 43 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN A 587 HIS ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 GLN A1210 HIS A1230 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12213 Z= 0.228 Angle : 0.518 6.667 16874 Z= 0.290 Chirality : 0.039 0.203 1894 Planarity : 0.003 0.040 1841 Dihedral : 18.444 172.471 2619 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.92 % Allowed : 5.96 % Favored : 93.13 % 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: 0.58 (0.24), residues: 1201 helix: 0.97 (0.21), residues: 611 sheet: -0.32 (0.39), residues: 157 loop : 0.01 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.017 0.001 PHE A 180 TYR 0.016 0.001 TYR A 544 ARG 0.007 0.001 ARG A 660 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 54 time to evaluate : 1.350 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 60 average time/residue: 1.4988 time to fit residues: 97.9320 Evaluate side-chains 44 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 483 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 79 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 HIS A1211 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12213 Z= 0.217 Angle : 0.488 7.605 16874 Z= 0.271 Chirality : 0.038 0.207 1894 Planarity : 0.003 0.032 1841 Dihedral : 18.387 161.989 2619 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.01 % Allowed : 6.87 % Favored : 92.12 % 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: 1.08 (0.24), residues: 1201 helix: 1.47 (0.21), residues: 611 sheet: -0.27 (0.39), residues: 157 loop : 0.16 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.002 0.001 HIS A 640 PHE 0.016 0.001 PHE A 180 TYR 0.016 0.001 TYR A 544 ARG 0.006 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 55 time to evaluate : 1.245 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 62 average time/residue: 1.4193 time to fit residues: 95.7603 Evaluate side-chains 49 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 603 SER Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1086 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 12213 Z= 0.349 Angle : 0.529 6.058 16874 Z= 0.292 Chirality : 0.041 0.224 1894 Planarity : 0.003 0.031 1841 Dihedral : 18.426 150.676 2619 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.56 % Allowed : 7.24 % Favored : 91.20 % 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: 1.29 (0.25), residues: 1201 helix: 1.70 (0.21), residues: 601 sheet: -0.37 (0.38), residues: 157 loop : 0.30 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A1219 PHE 0.018 0.002 PHE A 757 TYR 0.018 0.001 TYR A 544 ARG 0.006 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 43 time to evaluate : 1.248 Fit side-chains REVERT: A 630 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6963 (mtpm) outliers start: 17 outliers final: 9 residues processed: 56 average time/residue: 1.4609 time to fit residues: 89.2306 Evaluate side-chains 51 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1211 ASN Chi-restraints excluded: chain A residue 1231 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12213 Z= 0.215 Angle : 0.475 5.916 16874 Z= 0.263 Chirality : 0.038 0.205 1894 Planarity : 0.003 0.029 1841 Dihedral : 18.370 149.977 2619 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.19 % Allowed : 8.07 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1201 helix: 1.83 (0.21), residues: 606 sheet: -0.33 (0.38), residues: 157 loop : 0.34 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.002 0.001 HIS A 640 PHE 0.015 0.001 PHE A 180 TYR 0.016 0.001 TYR A 544 ARG 0.007 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 1.069 Fit side-chains REVERT: A 630 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6938 (mtpm) outliers start: 13 outliers final: 6 residues processed: 56 average time/residue: 1.4263 time to fit residues: 87.0877 Evaluate side-chains 51 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12213 Z= 0.251 Angle : 0.494 7.594 16874 Z= 0.273 Chirality : 0.039 0.211 1894 Planarity : 0.003 0.030 1841 Dihedral : 18.398 150.351 2619 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.28 % Allowed : 8.52 % Favored : 90.19 % 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: 1.42 (0.25), residues: 1201 helix: 1.82 (0.21), residues: 613 sheet: -0.33 (0.38), residues: 157 loop : 0.30 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 253 PHE 0.015 0.001 PHE A 180 TYR 0.017 0.001 TYR A 544 ARG 0.007 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 1.300 Fit side-chains REVERT: A 630 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6872 (mtpm) outliers start: 14 outliers final: 8 residues processed: 55 average time/residue: 1.3480 time to fit residues: 81.4994 Evaluate side-chains 52 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 77 optimal weight: 0.0970 chunk 75 optimal weight: 0.0040 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 830 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12213 Z= 0.152 Angle : 0.460 6.908 16874 Z= 0.254 Chirality : 0.036 0.192 1894 Planarity : 0.002 0.029 1841 Dihedral : 18.354 149.830 2619 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.10 % Allowed : 9.07 % Favored : 89.83 % 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: 1.59 (0.25), residues: 1201 helix: 1.96 (0.21), residues: 614 sheet: -0.20 (0.39), residues: 157 loop : 0.36 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.002 0.001 HIS A 640 PHE 0.014 0.001 PHE A 180 TYR 0.015 0.001 TYR A 544 ARG 0.005 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 55 time to evaluate : 1.210 Fit side-chains REVERT: A 1 MET cc_start: 0.4545 (ttp) cc_final: 0.4131 (mtm) REVERT: A 630 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.6875 (mtpm) outliers start: 12 outliers final: 6 residues processed: 64 average time/residue: 1.3054 time to fit residues: 91.5899 Evaluate side-chains 54 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12213 Z= 0.279 Angle : 0.509 8.712 16874 Z= 0.279 Chirality : 0.039 0.212 1894 Planarity : 0.003 0.030 1841 Dihedral : 18.386 150.382 2619 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.01 % Allowed : 10.17 % Favored : 88.82 % 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: 1.53 (0.25), residues: 1201 helix: 1.93 (0.21), residues: 614 sheet: -0.29 (0.39), residues: 157 loop : 0.32 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 480 HIS 0.003 0.001 HIS A 253 PHE 0.016 0.001 PHE A 757 TYR 0.018 0.001 TYR A 544 ARG 0.006 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 1.198 Fit side-chains REVERT: A 1 MET cc_start: 0.4705 (ttp) cc_final: 0.4298 (mtm) REVERT: A 630 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6873 (mtpm) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 1.3099 time to fit residues: 75.2742 Evaluate side-chains 54 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 45 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 114 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12213 Z= 0.191 Angle : 0.479 8.849 16874 Z= 0.263 Chirality : 0.037 0.198 1894 Planarity : 0.003 0.029 1841 Dihedral : 18.349 149.937 2619 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.28 % Allowed : 9.90 % Favored : 88.82 % 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: 1.61 (0.25), residues: 1201 helix: 1.99 (0.21), residues: 615 sheet: -0.21 (0.39), residues: 157 loop : 0.35 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.002 0.001 HIS A 640 PHE 0.014 0.001 PHE A 180 TYR 0.016 0.001 TYR A 544 ARG 0.006 0.000 ARG A 307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 1.290 Fit side-chains REVERT: A 1 MET cc_start: 0.4586 (OUTLIER) cc_final: 0.4247 (mtm) REVERT: A 630 LYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6879 (mtpm) outliers start: 14 outliers final: 9 residues processed: 56 average time/residue: 1.3329 time to fit residues: 82.2226 Evaluate side-chains 57 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 485 HIS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 742 GLU Chi-restraints excluded: chain A residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 12213 Z= 0.477 Angle : 0.588 7.931 16874 Z= 0.318 Chirality : 0.044 0.240 1894 Planarity : 0.003 0.031 1841 Dihedral : 18.485 150.502 2619 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.19 % Allowed : 10.08 % Favored : 88.73 % 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: 1.38 (0.25), residues: 1201 helix: 1.85 (0.21), residues: 607 sheet: -0.39 (0.39), residues: 157 loop : 0.22 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 480 HIS 0.003 0.001 HIS A 701 PHE 0.022 0.002 PHE A 757 TYR 0.021 0.002 TYR A 544 ARG 0.008 0.000 ARG A 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 1.283 Fit side-chains REVERT: A 1 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.4461 (ttm) REVERT: A 630 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6929 (mtpm) outliers start: 13 outliers final: 8 residues processed: 51 average time/residue: 1.3664 time to fit residues: 76.5317 Evaluate side-chains 52 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 442 ASN Chi-restraints excluded: chain A residue 461 ILE Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain A residue 1231 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 956 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.078305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.059719 restraints weight = 20945.167| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.01 r_work: 0.2612 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12213 Z= 0.200 Angle : 0.496 8.159 16874 Z= 0.270 Chirality : 0.038 0.204 1894 Planarity : 0.003 0.032 1841 Dihedral : 18.399 149.685 2619 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.82 % Allowed : 10.45 % Favored : 88.73 % 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 (0.25), residues: 1201 helix: 1.95 (0.21), residues: 614 sheet: -0.28 (0.39), residues: 157 loop : 0.34 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 480 HIS 0.003 0.001 HIS A 640 PHE 0.015 0.001 PHE A 180 TYR 0.015 0.001 TYR A 544 ARG 0.008 0.000 ARG A 307 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3124.60 seconds wall clock time: 57 minutes 4.09 seconds (3424.09 seconds total)