Starting phenix.real_space_refine on Mon Apr 8 05:50:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asg_15615/04_2024/8asg_15615.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asg_15615/04_2024/8asg_15615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asg_15615/04_2024/8asg_15615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asg_15615/04_2024/8asg_15615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asg_15615/04_2024/8asg_15615.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8asg_15615/04_2024/8asg_15615.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 16 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 7988 2.51 5 N 2202 2.21 5 O 2409 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A ASP 504": "OD1" <-> "OD2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A ASP 794": "OD1" <-> "OD2" Residue "A GLU 836": "OE1" <-> "OE2" Residue "A ASP 844": "OD1" <-> "OD2" Residue "A GLU 963": "OE1" <-> "OE2" Residue "A PHE 1056": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1141": "OD1" <-> "OD2" Residue "A GLU 1180": "OE1" <-> "OE2" Residue "A PHE 1423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1470": "OE1" <-> "OE2" Residue "A ASP 1472": "OD1" <-> "OD2" Residue "A PHE 1522": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12687 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12324 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1544, 12311 Classifications: {'peptide': 1544} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1484} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 1544, 12311 Classifications: {'peptide': 1544} Link IDs: {'PCIS': 2, 'PTRANS': 57, 'TRANS': 1484} Chain breaks: 8 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 12558 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Classifications: {'RNA': 2} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 1} Chain: "P" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 213 Classifications: {'RNA': 10} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "T" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.45, per 1000 atoms: 1.06 Number of scatterers: 12687 At special positions: 0 Unit cell: (101.15, 113.05, 122.4, 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 71 16.00 P 16 15.00 Mg 1 11.99 O 2409 8.00 N 2202 7.00 C 7988 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: 4.39 Conformation dependent library (CDL) restraints added in 4.4 seconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2908 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 54.2% alpha, 8.0% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 84 removed outlier: 3.646A pdb=" N PHE A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 removed outlier: 3.545A pdb=" N VAL A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.515A pdb=" N LEU A 138 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 removed outlier: 4.224A pdb=" N ILE A 153 " --> pdb=" O TYR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 209 Processing helix chain 'A' and resid 217 through 234 removed outlier: 3.535A pdb=" N LEU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 3.750A pdb=" N PHE A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 Processing helix chain 'A' and resid 262 through 286 Processing helix chain 'A' and resid 292 through 319 removed outlier: 3.777A pdb=" N ARG A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 removed outlier: 3.554A pdb=" N SER A 354 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET A 356 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP A 357 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 375 removed outlier: 3.601A pdb=" N LEU A 369 " --> pdb=" O TRP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 393 removed outlier: 3.751A pdb=" N GLU A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 400 removed outlier: 3.980A pdb=" N ASP A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 438 through 447 removed outlier: 3.683A pdb=" N HIS A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 465 Processing helix chain 'A' and resid 477 through 491 Processing helix chain 'A' and resid 499 through 511 removed outlier: 3.681A pdb=" N PHE A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 573 through 575 No H-bonds generated for 'chain 'A' and resid 573 through 575' Processing helix chain 'A' and resid 604 through 611 removed outlier: 4.227A pdb=" N ASN A 608 " --> pdb=" O CYS A 604 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 609 " --> pdb=" O LYS A 605 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 626 Processing helix chain 'A' and resid 638 through 655 Processing helix chain 'A' and resid 656 through 665 removed outlier: 3.666A pdb=" N GLU A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE A 663 " --> pdb=" O THR A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 671 removed outlier: 3.541A pdb=" N THR A 669 " --> pdb=" O LEU A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 675 Processing helix chain 'A' and resid 682 through 690 removed outlier: 3.652A pdb=" N LYS A 685 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET A 686 " --> pdb=" O PRO A 683 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 687 " --> pdb=" O GLN A 684 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 688 " --> pdb=" O LYS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 716 Processing helix chain 'A' and resid 742 through 750 removed outlier: 3.827A pdb=" N TRP A 750 " --> pdb=" O MET A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 removed outlier: 3.532A pdb=" N LYS A 756 " --> pdb=" O GLY A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 779 removed outlier: 4.096A pdb=" N TYR A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A 777 " --> pdb=" O LYS A 773 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 778 " --> pdb=" O ILE A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 removed outlier: 4.305A pdb=" N PHE A 787 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 822 removed outlier: 3.710A pdb=" N ARG A 820 " --> pdb=" O GLU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 840 removed outlier: 3.677A pdb=" N ASN A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS A 840 " --> pdb=" O GLU A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 860 through 865 removed outlier: 3.819A pdb=" N VAL A 864 " --> pdb=" O LEU A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 885 removed outlier: 3.998A pdb=" N LYS A 877 " --> pdb=" O LYS A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 904 Processing helix chain 'A' and resid 926 through 945 removed outlier: 3.987A pdb=" N VAL A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 942 " --> pdb=" O THR A 938 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 956 No H-bonds generated for 'chain 'A' and resid 954 through 956' Processing helix chain 'A' and resid 957 through 973 removed outlier: 4.300A pdb=" N ILE A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLU A 963 " --> pdb=" O ASN A 959 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY A 966 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 967 " --> pdb=" O GLU A 963 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 993 removed outlier: 3.766A pdb=" N HIS A 993 " --> pdb=" O TRP A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 removed outlier: 4.043A pdb=" N LEU A 998 " --> pdb=" O TYR A 994 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1009 removed outlier: 6.061A pdb=" N LYS A1009 " --> pdb=" O MET A1006 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1006 through 1009' Processing helix chain 'A' and resid 1010 through 1018 Processing helix chain 'A' and resid 1019 through 1022 removed outlier: 3.679A pdb=" N ARG A1022 " --> pdb=" O SER A1019 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1019 through 1022' Processing helix chain 'A' and resid 1029 through 1040 removed outlier: 3.657A pdb=" N LEU A1033 " --> pdb=" O ASP A1029 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A1039 " --> pdb=" O HIS A1035 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1058 removed outlier: 3.616A pdb=" N GLU A1050 " --> pdb=" O ASP A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1109 removed outlier: 3.543A pdb=" N SER A1100 " --> pdb=" O SER A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1155 removed outlier: 4.213A pdb=" N VAL A1143 " --> pdb=" O ASP A1139 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG A1144 " --> pdb=" O MET A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1161 through 1164 Processing helix chain 'A' and resid 1194 through 1200 removed outlier: 4.073A pdb=" N TRP A1198 " --> pdb=" O PRO A1194 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A1200 " --> pdb=" O LEU A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1228 removed outlier: 3.558A pdb=" N GLU A1216 " --> pdb=" O ALA A1212 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS A1225 " --> pdb=" O LEU A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 Processing helix chain 'A' and resid 1257 through 1268 removed outlier: 3.786A pdb=" N SER A1267 " --> pdb=" O GLY A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1284 removed outlier: 3.818A pdb=" N ALA A1284 " --> pdb=" O PRO A1281 " (cutoff:3.500A) Processing helix chain 'A' and resid 1288 through 1300 removed outlier: 3.546A pdb=" N ASN A1292 " --> pdb=" O GLY A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1311 removed outlier: 3.656A pdb=" N LYS A1305 " --> pdb=" O ASP A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1353 Processing helix chain 'A' and resid 1360 through 1367 removed outlier: 3.668A pdb=" N GLN A1364 " --> pdb=" O ASP A1360 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A1365 " --> pdb=" O TRP A1361 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A1366 " --> pdb=" O VAL A1362 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A1367 " --> pdb=" O GLU A1363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1360 through 1367' Processing helix chain 'A' and resid 1368 through 1373 removed outlier: 3.531A pdb=" N VAL A1371 " --> pdb=" O ASN A1368 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A1372 " --> pdb=" O PRO A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1383 through 1391 Processing helix chain 'A' and resid 1392 through 1400 removed outlier: 3.968A pdb=" N THR A1396 " --> pdb=" O SER A1392 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER A1397 " --> pdb=" O PRO A1393 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A1400 " --> pdb=" O THR A1396 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1403 No H-bonds generated for 'chain 'A' and resid 1401 through 1403' Processing helix chain 'A' and resid 1404 through 1411 Processing helix chain 'A' and resid 1412 through 1414 No H-bonds generated for 'chain 'A' and resid 1412 through 1414' Processing helix chain 'A' and resid 1438 through 1448 Processing helix chain 'A' and resid 1457 through 1465 removed outlier: 3.529A pdb=" N ARG A1462 " --> pdb=" O PRO A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1467 through 1478 Processing helix chain 'A' and resid 1514 through 1519 Processing helix chain 'A' and resid 1539 through 1546 removed outlier: 3.664A pdb=" N ALA A1543 " --> pdb=" O ASP A1539 " (cutoff:3.500A) Processing helix chain 'A' and resid 1563 through 1572 Processing helix chain 'A' and resid 1597 through 1604 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 25 removed outlier: 3.546A pdb=" N SER A 179 " --> pdb=" O GLY A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39 removed outlier: 3.726A pdb=" N ASP A 37 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 46 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 336 removed outlier: 3.503A pdb=" N ARG A 577 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 410 through 411 removed outlier: 3.525A pdb=" N PHE A 565 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 410 through 411 removed outlier: 3.525A pdb=" N PHE A 565 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 922 through 925 removed outlier: 3.720A pdb=" N ILE A 922 " --> pdb=" O PHE A 911 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 911 " --> pdb=" O ILE A 922 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N MET A 906 " --> pdb=" O LYS A1025 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N MET A1027 " --> pdb=" O MET A 906 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE A 908 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1123 removed outlier: 6.654A pdb=" N SER A 983 " --> pdb=" O VAL A1173 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A1173 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 986 through 987 removed outlier: 4.257A pdb=" N TYR A1166 " --> pdb=" O LYS A 987 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1178 through 1181 Processing sheet with id=AB1, first strand: chain 'A' and resid 1338 through 1339 Processing sheet with id=AB2, first strand: chain 'A' and resid 1486 through 1488 removed outlier: 3.568A pdb=" N LYS A1487 " --> pdb=" O SER A1610 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1496 through 1497 removed outlier: 3.552A pdb=" N GLY A1585 " --> pdb=" O VAL A1496 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1581 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 5.27 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3882 1.34 - 1.46: 2252 1.46 - 1.58: 6708 1.58 - 1.70: 32 1.70 - 1.82: 117 Bond restraints: 12991 Sorted by residual: bond pdb=" CB PRO A1466 " pdb=" CG PRO A1466 " ideal model delta sigma weight residual 1.492 1.653 -0.161 5.00e-02 4.00e+02 1.04e+01 bond pdb=" N PRO A1466 " pdb=" CD PRO A1466 " ideal model delta sigma weight residual 1.473 1.517 -0.044 1.40e-02 5.10e+03 9.86e+00 bond pdb=" N PRO A1466 " pdb=" CA PRO A1466 " ideal model delta sigma weight residual 1.466 1.434 0.033 1.13e-02 7.83e+03 8.35e+00 bond pdb=" CB PRO A 396 " pdb=" CG PRO A 396 " ideal model delta sigma weight residual 1.492 1.603 -0.111 5.00e-02 4.00e+02 4.93e+00 bond pdb=" CA PRO A1466 " pdb=" C PRO A1466 " ideal model delta sigma weight residual 1.520 1.537 -0.016 9.50e-03 1.11e+04 2.96e+00 ... (remaining 12986 not shown) Histogram of bond angle deviations from ideal: 95.94 - 103.56: 205 103.56 - 111.18: 5021 111.18 - 118.80: 5440 118.80 - 126.43: 6676 126.43 - 134.05: 270 Bond angle restraints: 17612 Sorted by residual: angle pdb=" CA PRO A1466 " pdb=" N PRO A1466 " pdb=" CD PRO A1466 " ideal model delta sigma weight residual 112.00 97.27 14.73 1.40e+00 5.10e-01 1.11e+02 angle pdb=" N PRO A1466 " pdb=" CD PRO A1466 " pdb=" CG PRO A1466 " ideal model delta sigma weight residual 103.20 95.94 7.26 1.50e+00 4.44e-01 2.34e+01 angle pdb=" CA PRO A 396 " pdb=" N PRO A 396 " pdb=" CD PRO A 396 " ideal model delta sigma weight residual 112.00 105.37 6.63 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C LEU A 118 " pdb=" N ASP A 119 " pdb=" CA ASP A 119 " ideal model delta sigma weight residual 124.31 131.27 -6.96 1.67e+00 3.59e-01 1.74e+01 angle pdb=" N THR A 499 " pdb=" CA THR A 499 " pdb=" C THR A 499 " ideal model delta sigma weight residual 113.12 107.96 5.16 1.25e+00 6.40e-01 1.70e+01 ... (remaining 17607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.89: 7666 34.89 - 69.77: 173 69.77 - 104.66: 21 104.66 - 139.55: 1 139.55 - 174.43: 3 Dihedral angle restraints: 7864 sinusoidal: 3374 harmonic: 4490 Sorted by residual: dihedral pdb=" O4' U T 5 " pdb=" C1' U T 5 " pdb=" N1 U T 5 " pdb=" C2 U T 5 " ideal model delta sinusoidal sigma weight residual 200.00 45.38 154.62 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" CA TYR A1110 " pdb=" C TYR A1110 " pdb=" N MET A1111 " pdb=" CA MET A1111 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLN A1095 " pdb=" C GLN A1095 " pdb=" N SER A1096 " pdb=" CA SER A1096 " ideal model delta harmonic sigma weight residual 180.00 157.70 22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1786 0.075 - 0.150: 153 0.150 - 0.224: 8 0.224 - 0.299: 3 0.299 - 0.374: 4 Chirality restraints: 1954 Sorted by residual: chirality pdb=" P G P 8 " pdb=" OP1 G P 8 " pdb=" OP2 G P 8 " pdb=" O5' G P 8 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.50e+00 chirality pdb=" P U D 29 " pdb=" OP1 U D 29 " pdb=" OP2 U D 29 " pdb=" O5' U D 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.78 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" CA PRO A1466 " pdb=" N PRO A1466 " pdb=" C PRO A1466 " pdb=" CB PRO A1466 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1951 not shown) Planarity restraints: 2188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1465 " 0.098 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO A1466 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO A1466 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A1466 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1383 " 0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LEU A1383 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU A1383 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU A1384 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 395 " -0.054 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO A 396 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 396 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 396 " -0.044 5.00e-02 4.00e+02 ... (remaining 2185 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 224 2.67 - 3.23: 12006 3.23 - 3.79: 19629 3.79 - 4.34: 26571 4.34 - 4.90: 43524 Nonbonded interactions: 101954 Sorted by model distance: nonbonded pdb=" OD1 ASP A1127 " pdb="MG MG A2101 " model vdw 2.114 2.170 nonbonded pdb=" OE1 GLU A 643 " pdb=" OG SER A 737 " model vdw 2.198 2.440 nonbonded pdb=" O ILE A 663 " pdb=" OG1 THR A 666 " model vdw 2.211 2.440 nonbonded pdb=" OE2 GLU A 625 " pdb=" OG SER A1231 " model vdw 2.248 2.440 nonbonded pdb=" OG SER A 173 " pdb=" O GLY A 176 " model vdw 2.264 2.440 ... (remaining 101949 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: 1.880 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: 7.120 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 48.170 Find NCS groups from input model: 0.330 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.003 0.161 12991 Z= 0.207 Angle : 0.772 14.734 17612 Z= 0.412 Chirality : 0.046 0.374 1954 Planarity : 0.006 0.135 2188 Dihedral : 15.816 174.435 4956 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.29 % Allowed : 0.37 % Favored : 99.34 % 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: -1.13 (0.20), residues: 1528 helix: 0.08 (0.19), residues: 720 sheet: -0.48 (0.55), residues: 102 loop : -1.67 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1547 HIS 0.007 0.001 HIS A 563 PHE 0.030 0.001 PHE A 649 TYR 0.021 0.001 TYR A 142 ARG 0.011 0.001 ARG A 871 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 186 time to evaluate : 1.483 Fit side-chains REVERT: A 156 ARG cc_start: 0.6874 (mmt90) cc_final: 0.6420 (mmm-85) REVERT: A 1308 TYR cc_start: 0.7998 (t80) cc_final: 0.7705 (t80) outliers start: 3 outliers final: 0 residues processed: 187 average time/residue: 0.2934 time to fit residues: 78.6475 Evaluate side-chains 153 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 9.9990 chunk 117 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 79 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 GLN ** A 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 HIS A 993 HIS ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1336 HIS A1378 ASN A1564 HIS A1604 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12991 Z= 0.193 Angle : 0.595 8.737 17612 Z= 0.303 Chirality : 0.041 0.199 1954 Planarity : 0.005 0.063 2188 Dihedral : 12.267 179.059 1927 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.66 % Allowed : 6.77 % Favored : 92.56 % 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: -0.51 (0.21), residues: 1528 helix: 0.78 (0.19), residues: 736 sheet: -0.19 (0.55), residues: 101 loop : -1.62 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1547 HIS 0.007 0.001 HIS A1091 PHE 0.025 0.001 PHE A 649 TYR 0.029 0.002 TYR A1110 ARG 0.008 0.000 ARG A 971 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 1.490 Fit side-chains revert: symmetry clash REVERT: A 156 ARG cc_start: 0.6992 (mmt90) cc_final: 0.6534 (mmt90) REVERT: A 1308 TYR cc_start: 0.8184 (t80) cc_final: 0.7880 (t80) REVERT: A 1462 ARG cc_start: 0.6629 (ttm-80) cc_final: 0.6425 (ttp-110) outliers start: 8 outliers final: 4 residues processed: 159 average time/residue: 0.2673 time to fit residues: 61.5532 Evaluate side-chains 150 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 870 HIS Chi-restraints excluded: chain A residue 936 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 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 516 GLN A 757 ASN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12991 Z= 0.212 Angle : 0.590 9.184 17612 Z= 0.298 Chirality : 0.041 0.211 1954 Planarity : 0.004 0.048 2188 Dihedral : 12.132 177.694 1927 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.81 % Allowed : 7.81 % Favored : 91.38 % 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: -0.32 (0.21), residues: 1528 helix: 1.03 (0.19), residues: 732 sheet: -0.22 (0.55), residues: 101 loop : -1.61 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1064 HIS 0.007 0.001 HIS A1091 PHE 0.023 0.001 PHE A 649 TYR 0.027 0.002 TYR A1110 ARG 0.007 0.000 ARG A1582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.456 Fit side-chains revert: symmetry clash REVERT: A 1110 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.7172 (p90) REVERT: A 1209 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7239 (mt-10) REVERT: A 1304 ARG cc_start: 0.6671 (mmm160) cc_final: 0.6354 (mtp180) outliers start: 10 outliers final: 5 residues processed: 161 average time/residue: 0.2709 time to fit residues: 63.4759 Evaluate side-chains 146 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1110 TYR Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 149 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS A 563 HIS A 757 ASN A 991 GLN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12991 Z= 0.207 Angle : 0.573 9.700 17612 Z= 0.290 Chirality : 0.040 0.209 1954 Planarity : 0.004 0.047 2188 Dihedral : 12.038 176.890 1927 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.88 % Allowed : 9.50 % Favored : 89.62 % 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 (0.21), residues: 1528 helix: 1.25 (0.19), residues: 726 sheet: -0.24 (0.53), residues: 102 loop : -1.57 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 520 HIS 0.007 0.001 HIS A1091 PHE 0.022 0.001 PHE A 649 TYR 0.026 0.002 TYR A1110 ARG 0.008 0.000 ARG A1462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 148 time to evaluate : 1.542 Fit side-chains revert: symmetry clash REVERT: A 888 TRP cc_start: 0.8434 (m100) cc_final: 0.8078 (m100) REVERT: A 1110 TYR cc_start: 0.7425 (OUTLIER) cc_final: 0.7188 (p90) REVERT: A 1209 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 1304 ARG cc_start: 0.6714 (mmm160) cc_final: 0.6452 (mtp180) outliers start: 11 outliers final: 6 residues processed: 156 average time/residue: 0.2726 time to fit residues: 61.5691 Evaluate side-chains 147 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 1110 TYR Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 0.0040 chunk 2 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.3980 chunk 134 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 447 HIS A 563 HIS ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12991 Z= 0.171 Angle : 0.565 11.120 17612 Z= 0.283 Chirality : 0.040 0.205 1954 Planarity : 0.004 0.047 2188 Dihedral : 11.950 176.456 1927 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.96 % Allowed : 10.60 % Favored : 88.44 % 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 (0.21), residues: 1528 helix: 1.31 (0.19), residues: 733 sheet: -0.24 (0.52), residues: 102 loop : -1.58 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 520 HIS 0.005 0.001 HIS A1091 PHE 0.022 0.001 PHE A 649 TYR 0.026 0.001 TYR A1110 ARG 0.007 0.000 ARG A1462 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 147 time to evaluate : 1.376 Fit side-chains revert: symmetry clash REVERT: A 888 TRP cc_start: 0.8410 (m100) cc_final: 0.8078 (m100) REVERT: A 1110 TYR cc_start: 0.7381 (OUTLIER) cc_final: 0.7171 (p90) REVERT: A 1209 GLU cc_start: 0.7433 (mt-10) cc_final: 0.7175 (mt-10) REVERT: A 1304 ARG cc_start: 0.6704 (mmm160) cc_final: 0.6456 (mtp180) outliers start: 12 outliers final: 8 residues processed: 156 average time/residue: 0.2734 time to fit residues: 62.1428 Evaluate side-chains 150 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1110 TYR Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 149 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS A 563 HIS A 757 ASN A 959 ASN B ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12991 Z= 0.250 Angle : 0.598 11.118 17612 Z= 0.300 Chirality : 0.041 0.209 1954 Planarity : 0.004 0.048 2188 Dihedral : 11.992 176.451 1927 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.18 % Allowed : 11.12 % Favored : 87.70 % 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: -0.15 (0.21), residues: 1528 helix: 1.28 (0.20), residues: 726 sheet: -0.29 (0.52), residues: 102 loop : -1.61 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 433 HIS 0.007 0.001 HIS A1091 PHE 0.021 0.001 PHE A 649 TYR 0.025 0.002 TYR A1110 ARG 0.007 0.000 ARG A 971 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 888 TRP cc_start: 0.8477 (m100) cc_final: 0.8073 (m100) REVERT: A 1304 ARG cc_start: 0.6765 (mmm160) cc_final: 0.6515 (mtp180) REVERT: A 1462 ARG cc_start: 0.6660 (ttm-80) cc_final: 0.6423 (ttp-110) REVERT: A 1582 ARG cc_start: 0.7146 (ttt-90) cc_final: 0.6756 (ttt90) outliers start: 15 outliers final: 7 residues processed: 154 average time/residue: 0.2636 time to fit residues: 59.2581 Evaluate side-chains 145 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 0.0870 chunk 83 optimal weight: 4.9990 chunk 149 optimal weight: 0.0040 chunk 93 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 HIS A 563 HIS A 757 ASN A1091 HIS A1378 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12991 Z= 0.175 Angle : 0.571 11.455 17612 Z= 0.285 Chirality : 0.040 0.214 1954 Planarity : 0.004 0.047 2188 Dihedral : 11.936 176.171 1927 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.33 % Allowed : 11.56 % Favored : 87.11 % 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 (0.21), residues: 1528 helix: 1.35 (0.20), residues: 732 sheet: -0.31 (0.52), residues: 103 loop : -1.61 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 520 HIS 0.005 0.001 HIS A1091 PHE 0.020 0.001 PHE A 649 TYR 0.028 0.001 TYR A1110 ARG 0.006 0.000 ARG A1462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: A 295 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: A 888 TRP cc_start: 0.8373 (m100) cc_final: 0.8010 (m100) REVERT: A 1304 ARG cc_start: 0.6733 (mmm160) cc_final: 0.6517 (mtp180) outliers start: 17 outliers final: 12 residues processed: 159 average time/residue: 0.2633 time to fit residues: 61.6123 Evaluate side-chains 155 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.2980 chunk 89 optimal weight: 0.6980 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 117 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12991 Z= 0.191 Angle : 0.580 11.919 17612 Z= 0.288 Chirality : 0.040 0.216 1954 Planarity : 0.004 0.048 2188 Dihedral : 11.933 175.776 1927 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.03 % Allowed : 12.59 % Favored : 86.38 % 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: -0.06 (0.22), residues: 1528 helix: 1.36 (0.19), residues: 734 sheet: -0.33 (0.52), residues: 103 loop : -1.60 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 520 HIS 0.006 0.001 HIS A 447 PHE 0.021 0.001 PHE A 649 TYR 0.026 0.001 TYR A1110 ARG 0.006 0.000 ARG A1462 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: A 295 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 888 TRP cc_start: 0.8393 (m100) cc_final: 0.8017 (m100) REVERT: A 1304 ARG cc_start: 0.6740 (mmm160) cc_final: 0.6426 (mtp180) REVERT: A 1582 ARG cc_start: 0.7057 (ttt-90) cc_final: 0.6667 (ttt90) outliers start: 13 outliers final: 11 residues processed: 150 average time/residue: 0.2705 time to fit residues: 59.0829 Evaluate side-chains 153 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 143 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A 757 ASN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12991 Z= 0.248 Angle : 0.613 12.319 17612 Z= 0.305 Chirality : 0.042 0.214 1954 Planarity : 0.004 0.049 2188 Dihedral : 11.999 175.724 1927 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.33 % Allowed : 12.89 % Favored : 85.79 % 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: -0.16 (0.21), residues: 1528 helix: 1.26 (0.19), residues: 730 sheet: -0.44 (0.52), residues: 103 loop : -1.61 (0.22), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 433 HIS 0.006 0.001 HIS A1186 PHE 0.019 0.001 PHE A 649 TYR 0.026 0.002 TYR A1110 ARG 0.006 0.000 ARG A1462 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: A 295 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: A 888 TRP cc_start: 0.8434 (m100) cc_final: 0.8069 (m100) REVERT: A 1304 ARG cc_start: 0.6709 (mmm160) cc_final: 0.6495 (mtp180) REVERT: A 1582 ARG cc_start: 0.7042 (ttt-90) cc_final: 0.6701 (ttt90) outliers start: 17 outliers final: 12 residues processed: 152 average time/residue: 0.2862 time to fit residues: 62.7183 Evaluate side-chains 154 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 936 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 122 optimal weight: 0.0970 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A 757 ASN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12991 Z= 0.209 Angle : 0.604 12.842 17612 Z= 0.299 Chirality : 0.041 0.217 1954 Planarity : 0.004 0.048 2188 Dihedral : 11.980 175.510 1927 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.10 % Allowed : 13.18 % Favored : 85.71 % 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: -0.17 (0.21), residues: 1528 helix: 1.25 (0.20), residues: 737 sheet: -0.35 (0.52), residues: 103 loop : -1.66 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 520 HIS 0.006 0.001 HIS A1186 PHE 0.019 0.001 PHE A 649 TYR 0.025 0.002 TYR A1110 ARG 0.004 0.000 ARG A1462 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 254 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 295 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: A 888 TRP cc_start: 0.8363 (m100) cc_final: 0.8024 (m100) REVERT: A 1304 ARG cc_start: 0.6723 (mmm160) cc_final: 0.6522 (mtp180) REVERT: A 1582 ARG cc_start: 0.7038 (ttt-90) cc_final: 0.6676 (ttt90) outliers start: 14 outliers final: 11 residues processed: 152 average time/residue: 0.2719 time to fit residues: 59.6544 Evaluate side-chains 152 residues out of total 1355 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 774 ILE Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1341 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 113 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 15 optimal weight: 0.0570 chunk 22 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 HIS A 757 ASN ** A1091 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.189371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.130700 restraints weight = 31033.931| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 3.53 r_work: 0.3232 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12991 Z= 0.162 Angle : 0.588 13.255 17612 Z= 0.291 Chirality : 0.040 0.221 1954 Planarity : 0.004 0.048 2188 Dihedral : 11.909 175.184 1927 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 1.03 % Allowed : 13.62 % Favored : 85.35 % 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 (0.22), residues: 1528 helix: 1.34 (0.20), residues: 741 sheet: -0.23 (0.53), residues: 103 loop : -1.59 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 520 HIS 0.005 0.001 HIS A 447 PHE 0.020 0.001 PHE A 649 TYR 0.025 0.001 TYR A1110 ARG 0.006 0.000 ARG A 971 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2895.11 seconds wall clock time: 53 minutes 29.06 seconds (3209.06 seconds total)