Starting phenix.real_space_refine on Sat Mar 16 02:11:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as7_15608/03_2024/8as7_15608_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as7_15608/03_2024/8as7_15608.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as7_15608/03_2024/8as7_15608_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as7_15608/03_2024/8as7_15608_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as7_15608/03_2024/8as7_15608_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as7_15608/03_2024/8as7_15608.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as7_15608/03_2024/8as7_15608.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as7_15608/03_2024/8as7_15608_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8as7_15608/03_2024/8as7_15608_updated.pdb" } resolution = 2.6 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= 0.005 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: 6 Type Number sf(0) Gaussians P 39 5.49 5 Mg 2 5.21 5 S 73 5.16 5 C 8364 2.51 5 N 2339 2.21 5 O 2614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ASP 310": "OD1" <-> "OD2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 586": "OD1" <-> "OD2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 831": "OE1" <-> "OE2" Residue "A PHE 934": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1029": "OD1" <-> "OD2" Residue "A PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1046": "OD1" <-> "OD2" Residue "A ASP 1061": "OD1" <-> "OD2" Residue "A PHE 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1120": "OD1" <-> "OD2" Residue "A ASP 1141": "OD1" <-> "OD2" Residue "A PHE 1147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1207": "OE1" <-> "OE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A TYR 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13431 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12586 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1575, 12550 Classifications: {'peptide': 1575} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1515} Chain breaks: 4 Conformer: "B" Number of residues, atoms: 1575, 12550 Classifications: {'peptide': 1575} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1515} Chain breaks: 4 bond proxies already assigned to first conformer: 12775 Chain: "P" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 363 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna3p_pur': 7, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "T" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 361 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 5, 'rna3p_pyr': 8} Link IDs: {'rna2p': 4, 'rna3p': 12} Chain: "G" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'p5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 49 Unusual residues: {' MG': 2, '2KH': 1, 'EPE': 1} Classifications: {'undetermined': 4, 'water': 3} Link IDs: {None: 6} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 12.92, per 1000 atoms: 0.96 Number of scatterers: 13431 At special positions: 0 Unit cell: (102.85, 107.95, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 73 16.00 P 39 15.00 Mg 2 11.99 O 2614 8.00 N 2339 7.00 C 8364 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: 5.60 Conformation dependent library (CDL) restraints added in 4.8 seconds 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 11 sheets defined 49.4% alpha, 7.8% beta 10 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 6.74 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 removed outlier: 3.723A pdb=" N CYS A 7 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 No H-bonds generated for 'chain 'A' and resid 78 through 81' Processing helix chain 'A' and resid 95 through 98 No H-bonds generated for 'chain 'A' and resid 95 through 98' Processing helix chain 'A' and resid 135 through 159 removed outlier: 4.433A pdb=" N ASP A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Proline residue: A 152 - end of helix removed outlier: 3.687A pdb=" N ASP A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 208 removed outlier: 4.129A pdb=" N MET A 208 " --> pdb=" O LYS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 218 through 233 Processing helix chain 'A' and resid 238 through 244 Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 263 through 284 Processing helix chain 'A' and resid 293 through 318 removed outlier: 3.703A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 356 No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 359 through 373 Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 417 through 426 removed outlier: 3.706A pdb=" N GLN A 426 " --> pdb=" O GLU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.843A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 464 Processing helix chain 'A' and resid 478 through 494 removed outlier: 4.614A pdb=" N MET A 493 " --> pdb=" O LYS A 489 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLN A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.680A pdb=" N TRP A 520 " --> pdb=" O GLN A 516 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 639 through 654 Processing helix chain 'A' and resid 657 through 674 removed outlier: 3.634A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 666 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 673 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE A 674 " --> pdb=" O GLN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 687 Processing helix chain 'A' and resid 697 through 715 Processing helix chain 'A' and resid 743 through 755 removed outlier: 3.612A pdb=" N TRP A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N GLY A 753 " --> pdb=" O SER A 749 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N TYR A 754 " --> pdb=" O TRP A 750 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR A 755 " --> pdb=" O TYR A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 778 removed outlier: 3.606A pdb=" N ILE A 774 " --> pdb=" O MET A 770 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 803 through 821 Processing helix chain 'A' and resid 825 through 839 Processing helix chain 'A' and resid 842 through 845 Processing helix chain 'A' and resid 856 through 858 No H-bonds generated for 'chain 'A' and resid 856 through 858' Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'A' and resid 874 through 883 Processing helix chain 'A' and resid 889 through 903 removed outlier: 4.521A pdb=" N GLY A 894 " --> pdb=" O ILE A 890 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLN A 895 " --> pdb=" O ASP A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 946 removed outlier: 4.039A pdb=" N GLY A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL A 936 " --> pdb=" O VAL A 932 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 946 " --> pdb=" O CYS A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 973 removed outlier: 4.116A pdb=" N SER A 960 " --> pdb=" O LEU A 957 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE A 961 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 963 " --> pdb=" O SER A 960 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 972 " --> pdb=" O SER A 969 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 973 " --> pdb=" O ALA A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 992 No H-bonds generated for 'chain 'A' and resid 989 through 992' Processing helix chain 'A' and resid 995 through 1004 Processing helix chain 'A' and resid 1008 through 1022 removed outlier: 4.576A pdb=" N ARG A1012 " --> pdb=" O LYS A1009 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP A1015 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A1017 " --> pdb=" O ILE A1014 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A1018 " --> pdb=" O TRP A1015 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET A1020 " --> pdb=" O ALA A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1037 Processing helix chain 'A' and resid 1047 through 1057 Processing helix chain 'A' and resid 1084 through 1108 Processing helix chain 'A' and resid 1139 through 1163 removed outlier: 3.887A pdb=" N VAL A1156 " --> pdb=" O LEU A1152 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LYS A1157 " --> pdb=" O LEU A1153 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE A1158 " --> pdb=" O HIS A1154 " (cutoff:3.500A) Proline residue: A1161 - end of helix Processing helix chain 'A' and resid 1195 through 1201 removed outlier: 3.857A pdb=" N ALA A1201 " --> pdb=" O ARG A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1227 Processing helix chain 'A' and resid 1232 through 1249 Processing helix chain 'A' and resid 1259 through 1265 Processing helix chain 'A' and resid 1271 through 1273 No H-bonds generated for 'chain 'A' and resid 1271 through 1273' Processing helix chain 'A' and resid 1281 through 1283 No H-bonds generated for 'chain 'A' and resid 1281 through 1283' Processing helix chain 'A' and resid 1289 through 1299 Processing helix chain 'A' and resid 1302 through 1315 Processing helix chain 'A' and resid 1334 through 1336 No H-bonds generated for 'chain 'A' and resid 1334 through 1336' Processing helix chain 'A' and resid 1342 through 1352 removed outlier: 3.665A pdb=" N ARG A1345 " --> pdb=" O TRP A1342 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS A1347 " --> pdb=" O ASP A1344 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR A1348 " --> pdb=" O ARG A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 Processing helix chain 'A' and resid 1369 through 1373 Processing helix chain 'A' and resid 1379 through 1390 Processing helix chain 'A' and resid 1393 through 1398 removed outlier: 3.825A pdb=" N SER A1398 " --> pdb=" O GLY A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1413 removed outlier: 3.695A pdb=" N ALA A1411 " --> pdb=" O ARG A1407 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A1412 " --> pdb=" O VAL A1408 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL A1413 " --> pdb=" O VAL A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1450 removed outlier: 4.025A pdb=" N MET A1450 " --> pdb=" O SER A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1463 Processing helix chain 'A' and resid 1468 through 1477 removed outlier: 3.709A pdb=" N LEU A1477 " --> pdb=" O ARG A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1513 through 1522 removed outlier: 3.575A pdb=" N SER A1518 " --> pdb=" O GLU A1514 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A1520 " --> pdb=" O LEU A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1545 removed outlier: 3.662A pdb=" N ALA A1543 " --> pdb=" O ASP A1539 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER A1544 " --> pdb=" O LYS A1540 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N PHE A1545 " --> pdb=" O LEU A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1564 through 1574 Processing helix chain 'A' and resid 1595 through 1603 Processing sheet with id= A, first strand: chain 'A' and resid 22 through 25 removed outlier: 3.502A pdb=" N SER A 179 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 122 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N GLY A 168 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 124 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N ILE A 170 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLU A 126 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 172 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N SER A 128 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 36 through 41 removed outlier: 3.624A pdb=" N ASP A 37 " --> pdb=" O ASP A 48 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.403A pdb=" N ARG A 409 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 569 through 571 Processing sheet with id= E, first strand: chain 'A' and resid 719 through 723 Processing sheet with id= F, first strand: chain 'A' and resid 921 through 925 removed outlier: 3.668A pdb=" N LEU A 910 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 978 through 984 Processing sheet with id= H, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id= I, first strand: chain 'A' and resid 1338 through 1340 Processing sheet with id= J, first strand: chain 'A' and resid 1486 through 1488 Processing sheet with id= K, first strand: chain 'A' and resid 1496 through 1503 removed outlier: 6.717A pdb=" N ARG A1579 " --> pdb=" O LEU A1502 " (cutoff:3.500A) 529 hydrogen bonds defined for protein. 1466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 6.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2120 1.31 - 1.44: 3878 1.44 - 1.56: 7589 1.56 - 1.69: 74 1.69 - 1.81: 121 Bond restraints: 13782 Sorted by residual: bond pdb=" C3' 2KH A2104 " pdb=" C4' 2KH A2104 " ideal model delta sigma weight residual 1.643 1.297 0.346 2.00e-02 2.50e+03 3.00e+02 bond pdb=" C4' 2KH A2104 " pdb=" O4' 2KH A2104 " ideal model delta sigma weight residual 1.310 1.614 -0.304 2.00e-02 2.50e+03 2.31e+02 bond pdb=" C1' 2KH A2104 " pdb=" O4' 2KH A2104 " ideal model delta sigma weight residual 1.561 1.308 0.253 2.00e-02 2.50e+03 1.60e+02 bond pdb=" C2' 2KH A2104 " pdb=" C3' 2KH A2104 " ideal model delta sigma weight residual 1.312 1.534 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1' 2KH A2104 " pdb=" N1 2KH A2104 " ideal model delta sigma weight residual 1.322 1.482 -0.160 2.00e-02 2.50e+03 6.38e+01 ... (remaining 13777 not shown) Histogram of bond angle deviations from ideal: 98.13 - 105.32: 400 105.32 - 112.52: 7169 112.52 - 119.71: 4703 119.71 - 126.91: 6256 126.91 - 134.10: 260 Bond angle restraints: 18788 Sorted by residual: angle pdb=" C LEU A1456 " pdb=" N ASN A1457 " pdb=" CA ASN A1457 " ideal model delta sigma weight residual 120.49 127.73 -7.24 1.42e+00 4.96e-01 2.60e+01 angle pdb=" N VAL A1507 " pdb=" CA VAL A1507 " pdb=" C VAL A1507 " ideal model delta sigma weight residual 106.53 111.40 -4.87 1.41e+00 5.03e-01 1.19e+01 angle pdb=" N CYS A1420 " pdb=" CA CYS A1420 " pdb=" C CYS A1420 " ideal model delta sigma weight residual 114.56 110.50 4.06 1.27e+00 6.20e-01 1.02e+01 angle pdb=" CA LEU A 118 " pdb=" CB LEU A 118 " pdb=" CG LEU A 118 " ideal model delta sigma weight residual 116.30 127.23 -10.93 3.50e+00 8.16e-02 9.75e+00 angle pdb=" C3 EPE A2103 " pdb=" N4 EPE A2103 " pdb=" C5 EPE A2103 " ideal model delta sigma weight residual 109.92 119.28 -9.36 3.00e+00 1.11e-01 9.73e+00 ... (remaining 18783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.35: 8053 31.35 - 62.70: 274 62.70 - 94.05: 57 94.05 - 125.41: 2 125.41 - 156.76: 4 Dihedral angle restraints: 8390 sinusoidal: 3797 harmonic: 4593 Sorted by residual: dihedral pdb=" O4' C T 19 " pdb=" C1' C T 19 " pdb=" N1 C T 19 " pdb=" C2 C T 19 " ideal model delta sinusoidal sigma weight residual 200.00 43.24 156.76 1 1.50e+01 4.44e-03 8.19e+01 dihedral pdb=" CA ASN A 959 " pdb=" C ASN A 959 " pdb=" N SER A 960 " pdb=" CA SER A 960 " ideal model delta harmonic sigma weight residual -180.00 -156.76 -23.24 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" O1A 2KH A2104 " pdb=" N3A 2KH A2104 " pdb=" PA 2KH A2104 " pdb=" PB 2KH A2104 " ideal model delta sinusoidal sigma weight residual -34.41 -167.97 133.56 1 3.00e+01 1.11e-03 1.80e+01 ... (remaining 8387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1707 0.049 - 0.098: 319 0.098 - 0.146: 69 0.146 - 0.195: 4 0.195 - 0.244: 3 Chirality restraints: 2102 Sorted by residual: chirality pdb=" CB ILE A 159 " pdb=" CA ILE A 159 " pdb=" CG1 ILE A 159 " pdb=" CG2 ILE A 159 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" C3' G T 13 " pdb=" C4' G T 13 " pdb=" O3' G T 13 " pdb=" C2' G T 13 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" C2' 2KH A2104 " pdb=" C1' 2KH A2104 " pdb=" C3' 2KH A2104 " pdb=" O2' 2KH A2104 " both_signs ideal model delta sigma weight residual False -2.39 -2.60 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2099 not shown) Planarity restraints: 2253 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 556 " 0.050 5.00e-02 4.00e+02 7.55e-02 9.11e+00 pdb=" N PRO A 557 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1457 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO A1458 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A1458 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1458 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 721 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 722 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 722 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 722 " -0.024 5.00e-02 4.00e+02 ... (remaining 2250 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 206 2.66 - 3.22: 11962 3.22 - 3.78: 21835 3.78 - 4.34: 30673 4.34 - 4.90: 48110 Nonbonded interactions: 112786 Sorted by model distance: nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2102 " model vdw 2.100 2.170 nonbonded pdb=" OE1 GLU A 387 " pdb=" OG SER A1417 " model vdw 2.225 2.440 nonbonded pdb=" O ALA A 986 " pdb="MG MG A2101 " model vdw 2.241 2.170 nonbonded pdb=" O LEU A1416 " pdb=" OG SER A1437 " model vdw 2.253 2.440 nonbonded pdb=" OG SER A1045 " pdb=" O2' A P 5 " model vdw 2.260 2.440 ... (remaining 112781 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=0.50 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: 1.850 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: 7.670 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 50.670 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 0.346 13782 Z= 0.354 Angle : 0.628 10.928 18788 Z= 0.339 Chirality : 0.041 0.244 2102 Planarity : 0.004 0.075 2253 Dihedral : 16.245 156.756 5420 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.29 % Allowed : 0.50 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: -0.09 (0.20), residues: 1570 helix: 0.72 (0.18), residues: 777 sheet: 0.77 (0.44), residues: 143 loop : -1.19 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 520 HIS 0.010 0.001 HIS A1190 PHE 0.022 0.001 PHE A 649 TYR 0.015 0.001 TYR A1166 ARG 0.006 0.000 ARG A 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 1.423 Fit side-chains REVERT: A 294 GLN cc_start: 0.7106 (mp10) cc_final: 0.6886 (mp10) REVERT: A 887 MET cc_start: 0.7626 (tpp) cc_final: 0.7288 (tpp) REVERT: A 1344 ASP cc_start: 0.5874 (m-30) cc_final: 0.5575 (m-30) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 1.6289 time to fit residues: 367.8346 Evaluate side-chains 169 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 608 ASN A 954 ASN A 959 ASN A 990 ASN A1190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 13782 Z= 0.312 Angle : 0.641 9.929 18788 Z= 0.331 Chirality : 0.043 0.201 2102 Planarity : 0.005 0.066 2253 Dihedral : 15.270 156.983 2311 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.88 % Allowed : 7.63 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.04 (0.20), residues: 1570 helix: 0.93 (0.18), residues: 775 sheet: 0.54 (0.42), residues: 145 loop : -1.18 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 520 HIS 0.010 0.002 HIS A1091 PHE 0.019 0.002 PHE A1048 TYR 0.022 0.002 TYR A1166 ARG 0.009 0.001 ARG A1304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 1.427 Fit side-chains REVERT: A 220 GLU cc_start: 0.6818 (tp30) cc_final: 0.6567 (tt0) REVERT: A 294 GLN cc_start: 0.7356 (mp10) cc_final: 0.7075 (mp10) REVERT: A 772 LYS cc_start: 0.8219 (tttt) cc_final: 0.7973 (ttmp) REVERT: A 1184 GLU cc_start: 0.7681 (tp30) cc_final: 0.7471 (tp30) REVERT: A 1261 PHE cc_start: 0.7582 (t80) cc_final: 0.7367 (t80) REVERT: A 1304 ARG cc_start: 0.7063 (mtp-110) cc_final: 0.6707 (ptt90) REVERT: A 1339 MET cc_start: 0.5866 (mtm) cc_final: 0.5570 (mtp) REVERT: A 1344 ASP cc_start: 0.5945 (m-30) cc_final: 0.5738 (p0) REVERT: A 1463 MET cc_start: 0.5558 (OUTLIER) cc_final: 0.5151 (tpt) outliers start: 37 outliers final: 17 residues processed: 187 average time/residue: 1.5770 time to fit residues: 317.8026 Evaluate side-chains 178 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 409 ARG Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1463 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 954 ASN A1190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13782 Z= 0.237 Angle : 0.565 8.605 18788 Z= 0.291 Chirality : 0.040 0.184 2102 Planarity : 0.004 0.063 2253 Dihedral : 15.142 156.717 2311 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.59 % Allowed : 9.79 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.20), residues: 1570 helix: 1.06 (0.19), residues: 779 sheet: 0.40 (0.41), residues: 145 loop : -1.18 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 520 HIS 0.006 0.001 HIS A1091 PHE 0.019 0.002 PHE A 649 TYR 0.019 0.002 TYR A1166 ARG 0.010 0.000 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.650 Fit side-chains REVERT: A 220 GLU cc_start: 0.6900 (tp30) cc_final: 0.6644 (tt0) REVERT: A 772 LYS cc_start: 0.8191 (tttt) cc_final: 0.7938 (ttmp) REVERT: A 1304 ARG cc_start: 0.7076 (mtp-110) cc_final: 0.6537 (ptt-90) REVERT: A 1339 MET cc_start: 0.5792 (mtm) cc_final: 0.5518 (mtp) REVERT: A 1344 ASP cc_start: 0.5956 (m-30) cc_final: 0.5746 (p0) REVERT: A 1456 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6441 (mt) REVERT: A 1463 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5217 (tpt) REVERT: A 1469 GLN cc_start: 0.7022 (tp-100) cc_final: 0.6380 (pm20) outliers start: 33 outliers final: 19 residues processed: 183 average time/residue: 1.5928 time to fit residues: 313.6654 Evaluate side-chains 180 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1463 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13782 Z= 0.255 Angle : 0.576 8.688 18788 Z= 0.297 Chirality : 0.041 0.190 2102 Planarity : 0.004 0.058 2253 Dihedral : 15.134 156.012 2311 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.74 % Allowed : 10.73 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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 (0.20), residues: 1570 helix: 1.02 (0.19), residues: 781 sheet: 0.23 (0.41), residues: 144 loop : -1.15 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 520 HIS 0.005 0.001 HIS A1419 PHE 0.019 0.002 PHE A 649 TYR 0.019 0.002 TYR A1166 ARG 0.009 0.000 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 166 time to evaluate : 1.665 Fit side-chains REVERT: A 79 ASN cc_start: 0.8625 (m-40) cc_final: 0.8113 (m110) REVERT: A 220 GLU cc_start: 0.6910 (tp30) cc_final: 0.6622 (tt0) REVERT: A 268 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7624 (mptt) REVERT: A 298 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6930 (mm-30) REVERT: A 772 LYS cc_start: 0.8193 (tttt) cc_final: 0.7937 (ttmp) REVERT: A 1111 MET cc_start: 0.6525 (pp-130) cc_final: 0.6258 (pp-130) REVERT: A 1304 ARG cc_start: 0.7074 (mtp-110) cc_final: 0.6722 (ptt90) REVERT: A 1339 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.5499 (mtp) REVERT: A 1344 ASP cc_start: 0.6000 (m-30) cc_final: 0.5792 (p0) REVERT: A 1385 LYS cc_start: 0.7645 (mttp) cc_final: 0.7390 (mttp) REVERT: A 1456 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6429 (mt) outliers start: 35 outliers final: 20 residues processed: 186 average time/residue: 1.4583 time to fit residues: 292.6190 Evaluate side-chains 186 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain A residue 1456 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 HIS A1604 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13782 Z= 0.299 Angle : 0.606 9.049 18788 Z= 0.314 Chirality : 0.042 0.193 2102 Planarity : 0.005 0.056 2253 Dihedral : 15.156 155.913 2311 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.95 % Allowed : 11.30 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.20), residues: 1570 helix: 1.01 (0.19), residues: 771 sheet: 0.13 (0.41), residues: 144 loop : -1.16 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 520 HIS 0.005 0.001 HIS A1419 PHE 0.020 0.002 PHE A 934 TYR 0.020 0.002 TYR A1166 ARG 0.012 0.001 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 1.306 Fit side-chains revert: symmetry clash REVERT: A 35 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6986 (p0) REVERT: A 220 GLU cc_start: 0.6912 (tp30) cc_final: 0.6643 (tt0) REVERT: A 772 LYS cc_start: 0.8201 (tttt) cc_final: 0.7951 (ttmp) REVERT: A 1111 MET cc_start: 0.6543 (pp-130) cc_final: 0.6341 (pp-130) REVERT: A 1339 MET cc_start: 0.5767 (OUTLIER) cc_final: 0.5513 (mtp) REVERT: A 1344 ASP cc_start: 0.6088 (m-30) cc_final: 0.5869 (p0) REVERT: A 1385 LYS cc_start: 0.7613 (mttp) cc_final: 0.7308 (mttp) REVERT: A 1456 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6428 (mt) outliers start: 38 outliers final: 24 residues processed: 187 average time/residue: 1.5219 time to fit residues: 306.7600 Evaluate side-chains 188 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 GLU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1339 MET Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1456 LEU Chi-restraints excluded: chain A residue 1502 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 0.0030 chunk 153 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 HIS A1604 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13782 Z= 0.226 Angle : 0.557 8.151 18788 Z= 0.288 Chirality : 0.040 0.185 2102 Planarity : 0.004 0.056 2253 Dihedral : 15.081 155.290 2311 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.52 % Allowed : 12.46 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.21 (0.21), residues: 1570 helix: 1.13 (0.19), residues: 773 sheet: 0.19 (0.41), residues: 144 loop : -1.07 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 520 HIS 0.004 0.001 HIS A 285 PHE 0.020 0.002 PHE A 649 TYR 0.018 0.002 TYR A1166 ARG 0.011 0.000 ARG A1304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.332 Fit side-chains REVERT: A 35 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.7006 (p0) REVERT: A 192 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.6904 (mpp) REVERT: A 220 GLU cc_start: 0.6863 (tp30) cc_final: 0.6561 (tt0) REVERT: A 723 ARG cc_start: 0.6301 (OUTLIER) cc_final: 0.5458 (ttp-170) REVERT: A 772 LYS cc_start: 0.8175 (tttt) cc_final: 0.7968 (ttmp) REVERT: A 1304 ARG cc_start: 0.7111 (mtp-110) cc_final: 0.6626 (ptt90) REVERT: A 1344 ASP cc_start: 0.6067 (m-30) cc_final: 0.5855 (p0) REVERT: A 1385 LYS cc_start: 0.7569 (mttp) cc_final: 0.7273 (mttp) REVERT: A 1456 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6515 (mt) REVERT: A 1469 GLN cc_start: 0.7138 (tp-100) cc_final: 0.6466 (pm20) outliers start: 32 outliers final: 20 residues processed: 184 average time/residue: 1.5844 time to fit residues: 316.9126 Evaluate side-chains 186 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 162 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1456 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 129 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 ASN A1190 HIS A1604 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13782 Z= 0.301 Angle : 0.606 8.663 18788 Z= 0.313 Chirality : 0.042 0.193 2102 Planarity : 0.005 0.053 2253 Dihedral : 15.075 155.388 2311 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.74 % Allowed : 12.67 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.08 (0.20), residues: 1570 helix: 1.04 (0.19), residues: 770 sheet: 0.09 (0.41), residues: 144 loop : -1.13 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 520 HIS 0.005 0.001 HIS A1419 PHE 0.020 0.002 PHE A 649 TYR 0.019 0.002 TYR A1166 ARG 0.011 0.001 ARG A1304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.361 Fit side-chains revert: symmetry clash REVERT: A 35 ASP cc_start: 0.7234 (OUTLIER) cc_final: 0.7008 (p0) REVERT: A 192 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.6928 (mpp) REVERT: A 220 GLU cc_start: 0.6891 (tp30) cc_final: 0.6594 (tt0) REVERT: A 772 LYS cc_start: 0.8186 (tttt) cc_final: 0.7977 (ttmp) REVERT: A 1111 MET cc_start: 0.6433 (pp-130) cc_final: 0.6192 (pp-130) REVERT: A 1344 ASP cc_start: 0.6121 (m-30) cc_final: 0.5896 (p0) REVERT: A 1385 LYS cc_start: 0.7624 (mttp) cc_final: 0.7424 (mttp) REVERT: A 1456 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6415 (mt) REVERT: A 1469 GLN cc_start: 0.7140 (tp-100) cc_final: 0.6470 (pm20) outliers start: 35 outliers final: 23 residues processed: 183 average time/residue: 1.5181 time to fit residues: 299.7299 Evaluate side-chains 187 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 161 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 290 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 497 GLU Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 GLU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1456 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 0.2980 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 0.6980 chunk 139 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 HIS A1604 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13782 Z= 0.196 Angle : 0.539 8.015 18788 Z= 0.277 Chirality : 0.039 0.182 2102 Planarity : 0.004 0.055 2253 Dihedral : 14.934 154.693 2311 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.30 % Allowed : 13.46 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.20 (0.21), residues: 1570 helix: 1.18 (0.19), residues: 775 sheet: 0.17 (0.40), residues: 148 loop : -1.17 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 520 HIS 0.004 0.001 HIS A 285 PHE 0.020 0.001 PHE A 649 TYR 0.016 0.002 TYR A1166 ARG 0.012 0.000 ARG A1304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 35 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.7038 (p0) REVERT: A 192 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.6814 (mpp) REVERT: A 220 GLU cc_start: 0.6824 (tp30) cc_final: 0.6539 (tt0) REVERT: A 723 ARG cc_start: 0.6329 (OUTLIER) cc_final: 0.5448 (ttp-170) REVERT: A 1111 MET cc_start: 0.6434 (pp-130) cc_final: 0.6200 (pp-130) REVERT: A 1304 ARG cc_start: 0.7117 (mtp-110) cc_final: 0.6637 (ptt90) REVERT: A 1344 ASP cc_start: 0.6040 (m-30) cc_final: 0.5832 (p0) REVERT: A 1346 LYS cc_start: 0.6759 (OUTLIER) cc_final: 0.6380 (mtpp) REVERT: A 1469 GLN cc_start: 0.7204 (tp-100) cc_final: 0.6465 (pm20) outliers start: 29 outliers final: 18 residues processed: 187 average time/residue: 1.5610 time to fit residues: 314.3448 Evaluate side-chains 181 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 159 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1126 ASP Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 GLU Chi-restraints excluded: chain A residue 1346 LYS Chi-restraints excluded: chain A residue 1413 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN A A 765 ASN A 959 ASN A1190 HIS A1604 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13782 Z= 0.314 Angle : 0.619 8.856 18788 Z= 0.319 Chirality : 0.043 0.195 2102 Planarity : 0.005 0.052 2253 Dihedral : 14.994 155.063 2311 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.30 % Allowed : 13.82 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.04 (0.20), residues: 1570 helix: 1.02 (0.19), residues: 771 sheet: 0.03 (0.41), residues: 148 loop : -1.17 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 520 HIS 0.005 0.001 HIS A1419 PHE 0.020 0.002 PHE A 649 TYR 0.019 0.002 TYR A1166 ARG 0.013 0.001 ARG A1189 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.593 Fit side-chains revert: symmetry clash REVERT: A 35 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.7013 (p0) REVERT: A 192 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.6944 (mpp) REVERT: A 220 GLU cc_start: 0.6917 (tp30) cc_final: 0.6583 (tt0) REVERT: A 1111 MET cc_start: 0.6473 (pp-130) cc_final: 0.6222 (pp-130) REVERT: A 1304 ARG cc_start: 0.7103 (mtp-110) cc_final: 0.6809 (ptt180) REVERT: A 1344 ASP cc_start: 0.6107 (m-30) cc_final: 0.5882 (p0) REVERT: A 1469 GLN cc_start: 0.7169 (tp-100) cc_final: 0.6453 (pm20) outliers start: 29 outliers final: 18 residues processed: 180 average time/residue: 1.5064 time to fit residues: 292.9282 Evaluate side-chains 179 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 368 CYS Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 GLU Chi-restraints excluded: chain A residue 1413 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 145 optimal weight: 0.0020 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1190 HIS A1604 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13782 Z= 0.153 Angle : 0.515 8.713 18788 Z= 0.263 Chirality : 0.038 0.176 2102 Planarity : 0.004 0.056 2253 Dihedral : 14.838 154.164 2311 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.44 % Allowed : 14.61 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.31 (0.21), residues: 1570 helix: 1.27 (0.19), residues: 772 sheet: 0.18 (0.41), residues: 148 loop : -1.09 (0.22), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 520 HIS 0.004 0.001 HIS A1190 PHE 0.021 0.001 PHE A 649 TYR 0.016 0.001 TYR A 24 ARG 0.013 0.000 ARG A1189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3140 Ramachandran restraints generated. 1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 165 time to evaluate : 1.630 Fit side-chains revert: symmetry clash REVERT: A 35 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.7031 (p0) REVERT: A 192 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.6767 (mpp) REVERT: A 220 GLU cc_start: 0.6711 (tp30) cc_final: 0.6402 (tt0) REVERT: A 777 MET cc_start: 0.8624 (mmp) cc_final: 0.8410 (tpt) REVERT: A 1304 ARG cc_start: 0.7091 (mtp-110) cc_final: 0.6633 (ptt90) REVERT: A 1469 GLN cc_start: 0.7100 (tp-100) cc_final: 0.6344 (pm20) REVERT: A 1487 LYS cc_start: 0.8151 (pttm) cc_final: 0.7940 (pttm) outliers start: 17 outliers final: 14 residues processed: 176 average time/residue: 1.5727 time to fit residues: 298.5189 Evaluate side-chains 177 residues out of total 1379 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 161 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ASP Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 723 ARG Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 887 MET Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1209 GLU Chi-restraints excluded: chain A residue 1262 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 18 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 7 optimal weight: 0.0070 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN A 959 ASN A1190 HIS A1604 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.169631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131258 restraints weight = 31947.612| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 4.46 r_work: 0.2936 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13782 Z= 0.160 Angle : 0.511 7.863 18788 Z= 0.261 Chirality : 0.038 0.176 2102 Planarity : 0.004 0.054 2253 Dihedral : 14.803 153.714 2311 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.44 % Allowed : 14.76 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % 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: 0.44 (0.21), residues: 1570 helix: 1.38 (0.19), residues: 772 sheet: 0.27 (0.42), residues: 146 loop : -1.03 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 520 HIS 0.005 0.001 HIS A1190 PHE 0.022 0.001 PHE A 649 TYR 0.014 0.001 TYR A1181 ARG 0.013 0.000 ARG A1189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5412.58 seconds wall clock time: 96 minutes 17.47 seconds (5777.47 seconds total)