Starting phenix.real_space_refine on Fri Feb 16 01:03:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d97_27257/02_2024/8d97_27257.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d97_27257/02_2024/8d97_27257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d97_27257/02_2024/8d97_27257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d97_27257/02_2024/8d97_27257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d97_27257/02_2024/8d97_27257.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d97_27257/02_2024/8d97_27257.pdb" } resolution = 3.8 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= 0.031 sd= 1.128 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 Zn 4 6.06 5 P 42 5.49 5 S 41 5.16 5 C 8625 2.51 5 N 2445 2.21 5 O 2717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 90": "OD1" <-> "OD2" Residue "A ARG 101": "NH1" <-> "NH2" Residue "A ARG 140": "NH1" <-> "NH2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A GLU 233": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ASP 309": "OD1" <-> "OD2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 390": "OD1" <-> "OD2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 710": "OE1" <-> "OE2" Residue "A GLU 743": "OE1" <-> "OE2" Residue "A ASP 744": "OD1" <-> "OD2" Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 765": "OE1" <-> "OE2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 939": "OE1" <-> "OE2" Residue "A GLU 967": "OE1" <-> "OE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A PHE 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1042": "OD1" <-> "OD2" Residue "A GLU 1050": "OE1" <-> "OE2" Residue "A TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1066": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A ASP 1098": "OD1" <-> "OD2" Residue "A TYR 1099": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "A ASP 1145": "OD1" <-> "OD2" Residue "A TYR 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1168": "OE1" <-> "OE2" Residue "A PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A GLU 1273": "OE1" <-> "OE2" Residue "A ASP 1279": "OD1" <-> "OD2" Residue "A PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1311": "OE1" <-> "OE2" Residue "A ASP 1317": "OD1" <-> "OD2" Residue "A TYR 1324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1327": "OD1" <-> "OD2" Residue "A ASP 1328": "OD1" <-> "OD2" Residue "A GLU 1335": "OE1" <-> "OE2" Residue "A ASP 1339": "OD1" <-> "OD2" Residue "A ASP 1346": "OD1" <-> "OD2" Residue "A GLU 1348": "OE1" <-> "OE2" Residue "A PHE 1353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1366": "OD1" <-> "OD2" Residue "A TYR 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1373": "OD1" <-> "OD2" Residue "A ASP 1395": "OD1" <-> "OD2" Residue "A ARG 1441": "NH1" <-> "NH2" Residue "A GLU 1446": "OE1" <-> "OE2" Residue "A ARG 1458": "NH1" <-> "NH2" Residue "A PHE 1461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1465": "OD1" <-> "OD2" Residue "A GLU 1469": "OE1" <-> "OE2" Residue "A PHE 1475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1518": "NH1" <-> "NH2" Residue "A PHE 1519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1526": "OE1" <-> "OE2" Residue "A PHE 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1663": "OD1" <-> "OD2" Residue "A PHE 1686": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13874 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 12990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1600, 12990 Classifications: {'peptide': 1600} Link IDs: {'PTRANS': 70, 'TRANS': 1529} Chain breaks: 8 Chain: "C" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 880 Classifications: {'RNA': 42} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 11, 'rna3p_pur': 5, 'rna3p_pyr': 15} Link IDs: {'rna2p': 21, 'rna3p': 20} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 668 SG CYS A 83 42.188 58.213 17.775 1.00112.54 S ATOM 939 SG CYS A 116 42.722 55.946 14.103 1.00121.93 S ATOM 985 SG CYS A 122 44.991 56.202 17.287 1.00100.15 S ATOM 1009 SG CYS A 125 41.791 54.844 17.275 1.00 97.33 S ATOM 3703 SG CYS A 486 34.125 74.468 46.993 1.00 79.62 S ATOM 3771 SG CYS A 496 35.438 72.708 43.943 1.00 73.06 S ATOM 3785 SG CYS A 498 37.071 75.312 45.520 1.00 71.64 S ATOM 3807 SG CYS A 501 38.009 71.893 46.011 1.00 70.88 S ATOM 5778 SG CYS A 745 25.020 80.291 78.130 1.00140.63 S ATOM 5791 SG CYS A 747 28.461 81.408 78.582 1.00121.80 S ATOM 5813 SG CYS A 750 29.191 78.549 76.694 1.00105.45 S ATOM 7764 SG CYS A1013 31.267 68.320 113.568 1.00118.39 S ATOM 10846 SG CYS A1401 28.623 68.577 111.063 1.00125.65 S ATOM 10897 SG CYS A1409 30.301 71.505 112.762 1.00106.08 S ATOM 10914 SG CYS A1412 32.758 70.068 110.750 1.00102.04 S Time building chain proxies: 7.85, per 1000 atoms: 0.57 Number of scatterers: 13874 At special positions: 0 Unit cell: (88.596, 110.424, 186.18, 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) Zn 4 29.99 S 41 16.00 P 42 15.00 O 2717 8.00 N 2445 7.00 C 8625 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1160 " - pdb=" SG CYS A1166 " distance=2.03 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: 5.27 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 116 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 122 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 83 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 125 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 498 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 486 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 496 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 745 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 747 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1703 " - pdb=" ND1 HIS A 742 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1013 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1401 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1412 " pdb="ZN ZN A1704 " - pdb=" SG CYS A1409 " Number of angles added : 21 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 32.6% alpha, 22.5% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain 'A' and resid 22 through 26 Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 54 through 73 removed outlier: 3.935A pdb=" N VAL A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 163 through 168 removed outlier: 3.645A pdb=" N ILE A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 262 through 282 removed outlier: 3.524A pdb=" N ASP A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 298 removed outlier: 4.216A pdb=" N ARG A 289 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 296 " --> pdb=" O ALA A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 302 removed outlier: 4.489A pdb=" N GLY A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 299 through 302' Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.899A pdb=" N GLU A 307 " --> pdb=" O GLU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 345 Processing helix chain 'A' and resid 349 through 369 Processing helix chain 'A' and resid 466 through 483 removed outlier: 3.559A pdb=" N LEU A 470 " --> pdb=" O PRO A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 Processing helix chain 'A' and resid 564 through 575 Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.625A pdb=" N THR A 592 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 625 through 632 removed outlier: 3.503A pdb=" N LEU A 629 " --> pdb=" O LYS A 625 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU A 631 " --> pdb=" O LYS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 653 through 659 Processing helix chain 'A' and resid 681 through 688 Processing helix chain 'A' and resid 718 through 735 removed outlier: 3.560A pdb=" N PHE A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 removed outlier: 3.611A pdb=" N GLU A 774 " --> pdb=" O ASN A 771 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 775 " --> pdb=" O GLY A 772 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 771 through 775' Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.811A pdb=" N LYS A 799 " --> pdb=" O ASP A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 843 Processing helix chain 'A' and resid 868 through 877 Processing helix chain 'A' and resid 994 through 1011 removed outlier: 3.944A pdb=" N LEU A 998 " --> pdb=" O PRO A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1039 removed outlier: 3.740A pdb=" N LYS A1037 " --> pdb=" O ALA A1034 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR A1039 " --> pdb=" O GLU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1052 Processing helix chain 'A' and resid 1054 through 1058 removed outlier: 3.651A pdb=" N ARG A1058 " --> pdb=" O PRO A1055 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1069 Processing helix chain 'A' and resid 1083 through 1090 removed outlier: 3.991A pdb=" N SER A1087 " --> pdb=" O ARG A1083 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP A1088 " --> pdb=" O ARG A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1107 Processing helix chain 'A' and resid 1144 through 1148 Processing helix chain 'A' and resid 1152 through 1157 Processing helix chain 'A' and resid 1163 through 1201 removed outlier: 4.015A pdb=" N ARG A1167 " --> pdb=" O SER A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1210 Processing helix chain 'A' and resid 1228 through 1230 No H-bonds generated for 'chain 'A' and resid 1228 through 1230' Processing helix chain 'A' and resid 1327 through 1341 Processing helix chain 'A' and resid 1346 through 1354 Processing helix chain 'A' and resid 1395 through 1399 Processing helix chain 'A' and resid 1409 through 1415 Processing helix chain 'A' and resid 1458 through 1463 removed outlier: 4.457A pdb=" N SER A1462 " --> pdb=" O ARG A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1486 removed outlier: 3.888A pdb=" N ILE A1485 " --> pdb=" O GLY A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1496 removed outlier: 3.515A pdb=" N ARG A1493 " --> pdb=" O GLN A1489 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU A1494 " --> pdb=" O LEU A1490 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A1496 " --> pdb=" O ILE A1492 " (cutoff:3.500A) Processing helix chain 'A' and resid 1523 through 1535 Processing helix chain 'A' and resid 1581 through 1596 Processing helix chain 'A' and resid 1610 through 1613 removed outlier: 3.757A pdb=" N VAL A1613 " --> pdb=" O GLN A1610 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1610 through 1613' Processing helix chain 'A' and resid 1614 through 1624 Processing helix chain 'A' and resid 1668 through 1678 Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 148 removed outlier: 3.890A pdb=" N LEU A 153 " --> pdb=" O SER A 51 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER A 51 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 37 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP A 190 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N GLU A 17 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 13.243A pdb=" N ARG A 188 " --> pdb=" O GLU A 17 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 183 through 191 current: chain 'A' and resid 230 through 235 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 176 removed outlier: 6.181A pdb=" N SER A 169 " --> pdb=" O TRP A 190 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TRP A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A 171 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ARG A 188 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 173 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR A 186 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG A 175 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 13.243A pdb=" N ARG A 188 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N GLU A 17 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP A 190 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 37 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER A 51 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 153 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'A' and resid 105 through 106 removed outlier: 6.229A pdb=" N THR A 105 " --> pdb=" O VAL A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 508 removed outlier: 6.673A pdb=" N GLU A 410 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A 606 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 412 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 604 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 414 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 602 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 507 through 508 removed outlier: 6.673A pdb=" N GLU A 410 " --> pdb=" O GLU A 606 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU A 606 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE A 412 " --> pdb=" O ILE A 604 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE A 604 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A 414 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE A 602 " --> pdb=" O VAL A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 521 through 525 Processing sheet with id=AA8, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.234A pdb=" N PHE A 715 " --> pdb=" O LEU A 769 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG A 818 " --> pdb=" O GLU A 765 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU A 767 " --> pdb=" O LYS A 816 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS A 816 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU A 769 " --> pdb=" O LYS A 814 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LYS A 814 " --> pdb=" O LEU A 769 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 703 removed outlier: 3.551A pdb=" N ALA A 708 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 782 through 784 Processing sheet with id=AB2, first strand: chain 'A' and resid 915 through 916 Processing sheet with id=AB3, first strand: chain 'A' and resid 919 through 922 Processing sheet with id=AB4, first strand: chain 'A' and resid 986 through 987 removed outlier: 7.460A pdb=" N LEU A 991 " --> pdb=" O TYR A1431 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR A1431 " --> pdb=" O LEU A 991 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL A1512 " --> pdb=" O GLU A1432 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU A 945 " --> pdb=" O ASN A1521 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS A 952 " --> pdb=" O ILE A1559 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE A1559 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 954 " --> pdb=" O ILE A1557 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE A1557 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1555 " --> pdb=" O HIS A1542 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1424 through 1426 removed outlier: 6.060A pdb=" N LEU A 945 " --> pdb=" O ASN A1521 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N LYS A 952 " --> pdb=" O ILE A1559 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ILE A1559 " --> pdb=" O LYS A 952 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLU A 954 " --> pdb=" O ILE A1557 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE A1557 " --> pdb=" O GLU A 954 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A1564 " --> pdb=" O LYS A1575 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 981 through 982 removed outlier: 7.279A pdb=" N TYR A 982 " --> pdb=" O GLU A1505 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1323 through 1326 removed outlier: 4.546A pdb=" N LEU A1125 " --> pdb=" O VAL A1326 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A1380 " --> pdb=" O HIS A1371 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1131 through 1136 removed outlier: 8.876A pdb=" N VAL A1132 " --> pdb=" O VAL A1232 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA A1234 " --> pdb=" O VAL A1132 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ARG A1134 " --> pdb=" O ALA A1234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1255 through 1258 Processing sheet with id=AC1, first strand: chain 'A' and resid 1255 through 1258 removed outlier: 3.836A pdb=" N ARG A1292 " --> pdb=" O GLU A1282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1416 through 1417 497 hydrogen bonds defined for protein. 1368 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: 6.16 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3223 1.33 - 1.45: 3177 1.45 - 1.57: 7719 1.57 - 1.69: 83 1.69 - 1.81: 56 Bond restraints: 14258 Sorted by residual: bond pdb=" C ASP A 933 " pdb=" N ILE A 934 " ideal model delta sigma weight residual 1.335 1.317 0.018 1.41e-02 5.03e+03 1.55e+00 bond pdb=" C GLY A1115 " pdb=" O GLY A1115 " ideal model delta sigma weight residual 1.237 1.225 0.012 9.70e-03 1.06e+04 1.44e+00 bond pdb=" C3' G C 45 " pdb=" C2' G C 45 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.50e-02 4.44e+03 1.43e+00 bond pdb=" C4' G C 45 " pdb=" O4' G C 45 " ideal model delta sigma weight residual 1.451 1.434 0.017 1.50e-02 4.44e+03 1.27e+00 bond pdb=" C LYS A 976 " pdb=" O LYS A 976 " ideal model delta sigma weight residual 1.249 1.240 0.009 8.50e-03 1.38e+04 1.06e+00 ... (remaining 14253 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.13: 620 107.13 - 113.85: 7923 113.85 - 120.58: 5753 120.58 - 127.31: 4886 127.31 - 134.04: 215 Bond angle restraints: 19397 Sorted by residual: angle pdb=" C2' G C 45 " pdb=" C1' G C 45 " pdb=" N9 G C 45 " ideal model delta sigma weight residual 112.00 118.53 -6.53 1.50e+00 4.44e-01 1.89e+01 angle pdb=" N GLY A1472 " pdb=" CA GLY A1472 " pdb=" C GLY A1472 " ideal model delta sigma weight residual 110.29 115.52 -5.23 1.28e+00 6.10e-01 1.67e+01 angle pdb=" N LYS A 911 " pdb=" CA LYS A 911 " pdb=" C LYS A 911 " ideal model delta sigma weight residual 114.56 109.74 4.82 1.27e+00 6.20e-01 1.44e+01 angle pdb=" N ASN A1252 " pdb=" CA ASN A1252 " pdb=" C ASN A1252 " ideal model delta sigma weight residual 110.91 115.25 -4.34 1.17e+00 7.31e-01 1.38e+01 angle pdb=" C PRO A1435 " pdb=" N GLU A1436 " pdb=" CA GLU A1436 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 1.00e+01 ... (remaining 19392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.82: 8347 34.82 - 69.64: 281 69.64 - 104.46: 41 104.46 - 139.28: 1 139.28 - 174.10: 3 Dihedral angle restraints: 8673 sinusoidal: 4078 harmonic: 4595 Sorted by residual: dihedral pdb=" C4' G C 26 " pdb=" C3' G C 26 " pdb=" C2' G C 26 " pdb=" C1' G C 26 " ideal model delta sinusoidal sigma weight residual -35.00 31.58 -66.58 1 8.00e+00 1.56e-02 9.04e+01 dihedral pdb=" C5' G C 26 " pdb=" C4' G C 26 " pdb=" C3' G C 26 " pdb=" O3' G C 26 " ideal model delta sinusoidal sigma weight residual 147.00 83.00 64.00 1 8.00e+00 1.56e-02 8.43e+01 dihedral pdb=" O4' C C 22 " pdb=" C1' C C 22 " pdb=" N1 C C 22 " pdb=" C2 C C 22 " ideal model delta sinusoidal sigma weight residual 200.00 55.93 144.07 1 1.50e+01 4.44e-03 7.72e+01 ... (remaining 8670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1764 0.056 - 0.113: 271 0.113 - 0.169: 42 0.169 - 0.226: 1 0.226 - 0.282: 2 Chirality restraints: 2080 Sorted by residual: chirality pdb=" C3' G C 26 " pdb=" C4' G C 26 " pdb=" O3' G C 26 " pdb=" C2' G C 26 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C1' G C 45 " pdb=" O4' G C 45 " pdb=" C2' G C 45 " pdb=" N9 G C 45 " both_signs ideal model delta sigma weight residual False 2.46 2.19 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C2' G C 26 " pdb=" C3' G C 26 " pdb=" O2' G C 26 " pdb=" C1' G C 26 " both_signs ideal model delta sigma weight residual False -2.52 -2.73 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2077 not shown) Planarity restraints: 2367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G C 45 " 0.047 2.00e-02 2.50e+03 2.11e-02 1.34e+01 pdb=" N9 G C 45 " -0.053 2.00e-02 2.50e+03 pdb=" C8 G C 45 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G C 45 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G C 45 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G C 45 " 0.006 2.00e-02 2.50e+03 pdb=" O6 G C 45 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G C 45 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G C 45 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G C 45 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G C 45 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G C 45 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 957 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO A 958 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 958 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 958 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1684 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A1685 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A1685 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1685 " 0.024 5.00e-02 4.00e+02 ... (remaining 2364 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 303 2.67 - 3.23: 13187 3.23 - 3.79: 20312 3.79 - 4.34: 27173 4.34 - 4.90: 44303 Nonbonded interactions: 105278 Sorted by model distance: nonbonded pdb=" O CYS A 745 " pdb="ZN ZN A1703 " model vdw 2.113 2.230 nonbonded pdb=" NH1 ARG A 723 " pdb=" OP1 A C 32 " model vdw 2.189 2.520 nonbonded pdb=" O GLU A1455 " pdb=" O2' C C 42 " model vdw 2.190 2.440 nonbonded pdb=" O PRO A1668 " pdb=" OG1 THR A1671 " model vdw 2.192 2.440 nonbonded pdb=" O GLN A 904 " pdb=" NZ LYS A1622 " model vdw 2.195 2.520 ... (remaining 105273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 3.930 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 45.100 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 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 : 0.004 0.040 14258 Z= 0.273 Angle : 0.643 6.526 19397 Z= 0.396 Chirality : 0.043 0.282 2080 Planarity : 0.004 0.044 2367 Dihedral : 17.275 174.102 5724 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.18), residues: 1582 helix: -1.05 (0.21), residues: 453 sheet: -1.35 (0.29), residues: 262 loop : -2.03 (0.19), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 PHE 0.022 0.001 PHE A1085 TYR 0.014 0.001 TYR A 644 ARG 0.003 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 874 MET cc_start: 0.9169 (mtm) cc_final: 0.8432 (mtp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.3369 time to fit residues: 24.3955 Evaluate side-chains 28 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS A 264 HIS A 282 ASN A 323 HIS A 610 ASN A 866 ASN A1033 ASN A1076 ASN ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1140 ASN ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1207 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN A1487 GLN A1532 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14258 Z= 0.190 Angle : 0.507 6.722 19397 Z= 0.268 Chirality : 0.041 0.166 2080 Planarity : 0.004 0.042 2367 Dihedral : 15.774 169.055 2409 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.85 % Allowed : 8.42 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.20), residues: 1582 helix: 0.32 (0.24), residues: 461 sheet: -1.05 (0.29), residues: 270 loop : -1.46 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 PHE 0.017 0.001 PHE A1353 TYR 0.012 0.001 TYR A 644 ARG 0.004 0.000 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9204 (tpp) cc_final: 0.8910 (tpp) REVERT: A 583 MET cc_start: 0.8683 (mmm) cc_final: 0.7467 (mmm) REVERT: A 825 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: A 874 MET cc_start: 0.9129 (mtm) cc_final: 0.8418 (mtp) REVERT: A 1054 ASN cc_start: 0.2152 (OUTLIER) cc_final: 0.1939 (p0) REVERT: A 1436 GLU cc_start: 0.8750 (tt0) cc_final: 0.8485 (tt0) REVERT: A 1522 LEU cc_start: 0.9438 (mp) cc_final: 0.9211 (mp) outliers start: 12 outliers final: 3 residues processed: 46 average time/residue: 0.2727 time to fit residues: 20.5935 Evaluate side-chains 36 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 31 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1054 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 149 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 147 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 14258 Z= 0.425 Angle : 0.608 6.564 19397 Z= 0.317 Chirality : 0.044 0.184 2080 Planarity : 0.004 0.047 2367 Dihedral : 15.684 172.544 2409 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.42 % Allowed : 12.03 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.21), residues: 1582 helix: 0.77 (0.25), residues: 441 sheet: -1.16 (0.30), residues: 275 loop : -1.37 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1030 HIS 0.007 0.001 HIS A 138 PHE 0.021 0.002 PHE A1353 TYR 0.009 0.001 TYR A 644 ARG 0.004 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 32 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 MET cc_start: 0.9326 (tpp) cc_final: 0.8990 (tpp) REVERT: A 825 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8618 (m-10) REVERT: A 874 MET cc_start: 0.9136 (mtm) cc_final: 0.8446 (mtp) REVERT: A 1054 ASN cc_start: 0.2161 (OUTLIER) cc_final: 0.1946 (p0) REVERT: A 1458 ARG cc_start: 0.7588 (mmt180) cc_final: 0.6534 (mmm-85) outliers start: 20 outliers final: 10 residues processed: 49 average time/residue: 0.2593 time to fit residues: 21.4051 Evaluate side-chains 40 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 28 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 912 ASN Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1495 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 4.9990 chunk 112 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 100 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 141 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14258 Z= 0.199 Angle : 0.475 5.743 19397 Z= 0.252 Chirality : 0.040 0.149 2080 Planarity : 0.004 0.047 2367 Dihedral : 15.402 174.292 2409 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.27 % Allowed : 13.23 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.21), residues: 1582 helix: 1.03 (0.25), residues: 455 sheet: -0.91 (0.30), residues: 274 loop : -1.15 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 PHE 0.019 0.001 PHE A1353 TYR 0.011 0.001 TYR A 644 ARG 0.002 0.000 ARG A1053 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 31 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: A 210 HIS cc_start: 0.8959 (OUTLIER) cc_final: 0.8757 (t70) REVERT: A 583 MET cc_start: 0.8778 (mmm) cc_final: 0.7752 (mmm) REVERT: A 825 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8575 (m-10) REVERT: A 874 MET cc_start: 0.9143 (mtm) cc_final: 0.8487 (mtp) REVERT: A 1054 ASN cc_start: 0.2117 (OUTLIER) cc_final: 0.1907 (p0) REVERT: A 1436 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: A 1458 ARG cc_start: 0.7617 (mmt180) cc_final: 0.6771 (mmt180) outliers start: 18 outliers final: 9 residues processed: 46 average time/residue: 0.2409 time to fit residues: 18.4818 Evaluate side-chains 40 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 27 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 951 CYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1305 ASN Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1495 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14258 Z= 0.371 Angle : 0.557 6.037 19397 Z= 0.290 Chirality : 0.043 0.174 2080 Planarity : 0.004 0.050 2367 Dihedral : 15.430 173.535 2409 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.91 % Allowed : 14.51 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1582 helix: 1.23 (0.25), residues: 443 sheet: -0.92 (0.31), residues: 273 loop : -1.19 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 PHE 0.018 0.001 PHE A1353 TYR 0.010 0.001 TYR A 644 ARG 0.004 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 28 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9221 (tpp) cc_final: 0.8989 (tpp) REVERT: A 825 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8602 (m-10) REVERT: A 874 MET cc_start: 0.9131 (mtm) cc_final: 0.8476 (mtp) REVERT: A 1054 ASN cc_start: 0.2218 (OUTLIER) cc_final: 0.1989 (p0) REVERT: A 1436 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: A 1458 ARG cc_start: 0.7688 (mmt180) cc_final: 0.6982 (mmt180) outliers start: 27 outliers final: 16 residues processed: 51 average time/residue: 0.2379 time to fit residues: 20.4999 Evaluate side-chains 46 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 27 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 912 ASN Chi-restraints excluded: chain A residue 913 LYS Chi-restraints excluded: chain A residue 951 CYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1305 ASN Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1495 THR Chi-restraints excluded: chain A residue 1564 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14258 Z= 0.155 Angle : 0.454 5.510 19397 Z= 0.239 Chirality : 0.040 0.142 2080 Planarity : 0.003 0.048 2367 Dihedral : 15.264 173.506 2409 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.42 % Allowed : 14.79 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.21), residues: 1582 helix: 1.33 (0.25), residues: 455 sheet: -0.79 (0.31), residues: 274 loop : -1.00 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 PHE 0.014 0.001 PHE A1353 TYR 0.010 0.001 TYR A 644 ARG 0.002 0.000 ARG A1053 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 30 time to evaluate : 1.534 Fit side-chains revert: symmetry clash REVERT: A 825 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: A 874 MET cc_start: 0.9112 (mtm) cc_final: 0.8474 (mtp) REVERT: A 1054 ASN cc_start: 0.1723 (OUTLIER) cc_final: 0.1503 (p0) REVERT: A 1436 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: A 1458 ARG cc_start: 0.7698 (mmt180) cc_final: 0.6982 (mmt180) outliers start: 20 outliers final: 10 residues processed: 47 average time/residue: 0.2572 time to fit residues: 20.0388 Evaluate side-chains 40 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 27 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 951 CYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1305 ASN Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1495 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 158 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14258 Z= 0.395 Angle : 0.570 6.125 19397 Z= 0.297 Chirality : 0.043 0.176 2080 Planarity : 0.004 0.050 2367 Dihedral : 15.367 173.681 2409 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.77 % Allowed : 15.36 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.21), residues: 1582 helix: 1.40 (0.25), residues: 443 sheet: -0.88 (0.31), residues: 273 loop : -1.11 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1030 HIS 0.004 0.001 HIS A 781 PHE 0.017 0.002 PHE A 825 TYR 0.010 0.001 TYR A 644 ARG 0.004 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 28 time to evaluate : 1.561 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9243 (tpp) cc_final: 0.9023 (tpp) REVERT: A 651 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8679 (pp20) REVERT: A 825 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8605 (m-10) REVERT: A 874 MET cc_start: 0.9092 (mtm) cc_final: 0.8421 (mtp) REVERT: A 1054 ASN cc_start: 0.1726 (OUTLIER) cc_final: 0.1498 (p0) REVERT: A 1436 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8481 (tm-30) REVERT: A 1458 ARG cc_start: 0.7696 (mmt180) cc_final: 0.7020 (mmt180) outliers start: 25 outliers final: 14 residues processed: 49 average time/residue: 0.2398 time to fit residues: 19.7764 Evaluate side-chains 46 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 28 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 912 ASN Chi-restraints excluded: chain A residue 951 CYS Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1305 ASN Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1495 THR Chi-restraints excluded: chain A residue 1564 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 107 optimal weight: 9.9990 chunk 78 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14258 Z= 0.205 Angle : 0.477 6.068 19397 Z= 0.251 Chirality : 0.041 0.148 2080 Planarity : 0.004 0.050 2367 Dihedral : 15.241 173.514 2409 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.49 % Allowed : 15.71 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.21), residues: 1582 helix: 1.48 (0.25), residues: 449 sheet: -0.83 (0.31), residues: 274 loop : -1.00 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 PHE 0.015 0.001 PHE A 376 TYR 0.009 0.001 TYR A 644 ARG 0.002 0.000 ARG A1053 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 30 time to evaluate : 1.615 Fit side-chains revert: symmetry clash REVERT: A 31 MET cc_start: 0.9194 (tpp) cc_final: 0.8971 (tpp) REVERT: A 651 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8723 (pp20) REVERT: A 825 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8519 (m-10) REVERT: A 874 MET cc_start: 0.9116 (mtm) cc_final: 0.8492 (mtp) REVERT: A 981 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.7987 (p0) REVERT: A 1054 ASN cc_start: 0.1724 (OUTLIER) cc_final: 0.1505 (p0) REVERT: A 1436 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8455 (tm-30) REVERT: A 1458 ARG cc_start: 0.7689 (mmt180) cc_final: 0.7036 (mmt180) outliers start: 21 outliers final: 12 residues processed: 48 average time/residue: 0.3140 time to fit residues: 23.7780 Evaluate side-chains 44 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 27 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 912 ASN Chi-restraints excluded: chain A residue 951 CYS Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1305 ASN Chi-restraints excluded: chain A residue 1436 GLU Chi-restraints excluded: chain A residue 1495 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 147 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 0.4980 chunk 139 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14258 Z= 0.151 Angle : 0.447 5.508 19397 Z= 0.234 Chirality : 0.039 0.139 2080 Planarity : 0.003 0.051 2367 Dihedral : 15.090 173.831 2409 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.34 % Allowed : 15.92 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1582 helix: 1.59 (0.25), residues: 455 sheet: -0.70 (0.31), residues: 272 loop : -0.87 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 PHE 0.013 0.001 PHE A1353 TYR 0.009 0.001 TYR A 644 ARG 0.009 0.000 ARG A1583 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 32 time to evaluate : 1.477 Fit side-chains revert: symmetry clash REVERT: A 825 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: A 874 MET cc_start: 0.9079 (mtm) cc_final: 0.8477 (mtp) REVERT: A 981 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8048 (p0) REVERT: A 1054 ASN cc_start: 0.1682 (OUTLIER) cc_final: 0.1449 (p0) REVERT: A 1436 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8371 (tm-30) REVERT: A 1458 ARG cc_start: 0.7748 (mmt180) cc_final: 0.7072 (mmt180) REVERT: A 1633 LYS cc_start: 0.8933 (mmmt) cc_final: 0.8723 (mmmt) outliers start: 19 outliers final: 8 residues processed: 48 average time/residue: 0.2685 time to fit residues: 20.9610 Evaluate side-chains 42 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 30 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 981 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 6.9990 chunk 155 optimal weight: 0.0970 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 163 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14258 Z= 0.425 Angle : 0.587 8.151 19397 Z= 0.305 Chirality : 0.044 0.177 2080 Planarity : 0.004 0.052 2367 Dihedral : 15.266 173.878 2409 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.06 % Allowed : 16.63 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.21), residues: 1582 helix: 1.57 (0.25), residues: 443 sheet: -0.79 (0.31), residues: 268 loop : -1.05 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 PHE 0.019 0.002 PHE A 376 TYR 0.010 0.001 TYR A 616 ARG 0.005 0.000 ARG A1583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3164 Ramachandran restraints generated. 1582 Oldfield, 0 Emsley, 1582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 30 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 825 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8616 (m-10) REVERT: A 874 MET cc_start: 0.9143 (mtm) cc_final: 0.8516 (mtp) REVERT: A 1054 ASN cc_start: 0.1744 (OUTLIER) cc_final: 0.1514 (p0) REVERT: A 1436 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8482 (tm-30) REVERT: A 1458 ARG cc_start: 0.7764 (mmt180) cc_final: 0.7110 (mmt180) REVERT: A 1633 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8792 (mmmt) outliers start: 15 outliers final: 11 residues processed: 43 average time/residue: 0.2920 time to fit residues: 20.2386 Evaluate side-chains 43 residues out of total 1413 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 29 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 652 CYS Chi-restraints excluded: chain A residue 749 MET Chi-restraints excluded: chain A residue 825 PHE Chi-restraints excluded: chain A residue 871 PHE Chi-restraints excluded: chain A residue 912 ASN Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1039 TYR Chi-restraints excluded: chain A residue 1044 ASN Chi-restraints excluded: chain A residue 1054 ASN Chi-restraints excluded: chain A residue 1305 ASN Chi-restraints excluded: chain A residue 1436 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.0980 chunk 138 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 54 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1532 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.123740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.074301 restraints weight = 37478.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.076170 restraints weight = 19338.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.077101 restraints weight = 13744.938| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14258 Z= 0.150 Angle : 0.462 8.030 19397 Z= 0.242 Chirality : 0.040 0.155 2080 Planarity : 0.004 0.050 2367 Dihedral : 15.129 173.390 2409 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 0.99 % Allowed : 16.91 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.21), residues: 1582 helix: 1.63 (0.26), residues: 454 sheet: -0.70 (0.31), residues: 267 loop : -0.90 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1030 HIS 0.005 0.001 HIS A 781 PHE 0.012 0.001 PHE A1353 TYR 0.010 0.001 TYR A 644 ARG 0.007 0.000 ARG A1583 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2151.24 seconds wall clock time: 41 minutes 55.85 seconds (2515.85 seconds total)