Starting phenix.real_space_refine on Mon Dec 11 08:40:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/12_2023/8wea_37476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/12_2023/8wea_37476.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/12_2023/8wea_37476_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/12_2023/8wea_37476_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/12_2023/8wea_37476_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/12_2023/8wea_37476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/12_2023/8wea_37476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/12_2023/8wea_37476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wea_37476/12_2023/8wea_37476_updated.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= -0.001 sd= 0.081 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 Ca 2 9.91 5 Br 1 7.06 5 S 92 5.16 5 C 11099 2.51 5 N 2826 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 127": "OE1" <-> "OE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 584": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 591": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A PHE 659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A GLU 681": "OE1" <-> "OE2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A PHE 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 737": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 899": "OD1" <-> "OD2" Residue "A PHE 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 921": "OD1" <-> "OD2" Residue "A TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1076": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1242": "OE1" <-> "OE2" Residue "A PHE 1282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1317": "OD1" <-> "OD2" Residue "A GLU 1464": "OE1" <-> "OE2" Residue "A GLU 1482": "OE1" <-> "OE2" Residue "A PHE 1499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "A PHE 1611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1627": "OE1" <-> "OE2" Residue "A GLU 1631": "OE1" <-> "OE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D ASP 59": "OD1" <-> "OD2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D GLU 105": "OE1" <-> "OE2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 278": "OE1" <-> "OE2" Residue "D ASP 286": "OD1" <-> "OD2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D ASP 320": "OD1" <-> "OD2" Residue "D GLU 366": "OE1" <-> "OE2" Residue "D PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D GLU 555": "OE1" <-> "OE2" Residue "D GLU 565": "OE1" <-> "OE2" Residue "D GLU 573": "OE1" <-> "OE2" Residue "D GLU 585": "OE1" <-> "OE2" Residue "D ASP 596": "OD1" <-> "OD2" Residue "D GLU 636": "OE1" <-> "OE2" Residue "D TYR 644": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 655": "OE1" <-> "OE2" Residue "D ASP 665": "OD1" <-> "OD2" Residue "D TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 674": "OD1" <-> "OD2" Residue "D GLU 685": "OE1" <-> "OE2" Residue "D PHE 686": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 737": "OD1" <-> "OD2" Residue "D GLU 747": "OE1" <-> "OE2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D ASP 771": "OD1" <-> "OD2" Residue "D TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 899": "OD1" <-> "OD2" Residue "D TYR 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 17188 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 9335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1206, 9335 Classifications: {'peptide': 1206} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 39, 'TRANS': 1166} Chain breaks: 12 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 400 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 211 Chain: "D" Number of atoms: 7570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7570 Classifications: {'peptide': 948} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 907} Chain breaks: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 72 Unusual residues: {' CA': 1, '9Z9': 1, 'WB9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.43, per 1000 atoms: 0.61 Number of scatterers: 17188 At special positions: 0 Unit cell: (137.022, 141.478, 176.012, 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) Br 1 34.99 Ca 2 19.99 S 92 16.00 O 3168 8.00 N 2826 7.00 C 11099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 326 " distance=2.02 Simple disulfide: pdb=" SG CYS A 316 " - pdb=" SG CYS A 332 " distance=2.02 Simple disulfide: pdb=" SG CYS A1078 " - pdb=" SG CYS A1089 " distance=2.03 Simple disulfide: pdb=" SG CYS A1479 " - pdb=" SG CYS A1495 " distance=2.04 Simple disulfide: pdb=" SG CYS D 303 " - pdb=" SG CYS D1044 " distance=2.03 Simple disulfide: pdb=" SG CYS D 404 " - pdb=" SG CYS D1071 " distance=2.03 Simple disulfide: pdb=" SG CYS D 667 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 904 " - pdb=" SG CYS D 974 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1026 " distance=2.03 Simple disulfide: pdb=" SG CYS D 999 " - pdb=" SG CYS D1024 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " NAG B 3 " " NAG C 1 " - " NAG C 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG E 3 " - " NAG E 4 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG B 1 " - " ASN D 184 " " NAG C 1 " - " ASN D 348 " " NAG D1202 " - " ASN D 92 " " NAG D1203 " - " ASN D 781 " " NAG E 1 " - " ASN D 468 " " NAG F 1 " - " ASN D 613 " " NAG G 1 " - " ASN D 895 " Time building additional restraints: 7.66 Conformation dependent library (CDL) restraints added in 3.6 seconds 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4074 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 11 sheets defined 50.1% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 123 through 138 removed outlier: 3.513A pdb=" N ILE A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE A 130 " --> pdb=" O PHE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.610A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.654A pdb=" N PHE A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N THR A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 216 removed outlier: 3.590A pdb=" N VAL A 205 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 207 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 240 through 250 Proline residue: A 244 - end of helix removed outlier: 4.073A pdb=" N GLY A 250 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 265 removed outlier: 4.103A pdb=" N VAL A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N VAL A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 269 No H-bonds generated for 'chain 'A' and resid 267 through 269' Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.687A pdb=" N LEU A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 360 Processing helix chain 'A' and resid 365 through 376 Processing helix chain 'A' and resid 381 through 392 removed outlier: 3.713A pdb=" N PHE A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 418 removed outlier: 3.638A pdb=" N LEU A 399 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 445 removed outlier: 4.033A pdb=" N TRP A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 522 Processing helix chain 'A' and resid 524 through 543 Processing helix chain 'A' and resid 550 through 577 removed outlier: 3.962A pdb=" N VAL A 555 " --> pdb=" O TRP A 551 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TYR A 576 " --> pdb=" O LEU A 572 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 587 through 606 Processing helix chain 'A' and resid 613 through 629 removed outlier: 3.695A pdb=" N LEU A 624 " --> pdb=" O ARG A 620 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU A 625 " --> pdb=" O CYS A 621 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ARG A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 650 removed outlier: 4.374A pdb=" N ASN A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 672 Processing helix chain 'A' and resid 692 through 704 Processing helix chain 'A' and resid 708 through 718 Processing helix chain 'A' and resid 730 through 754 removed outlier: 3.750A pdb=" N ILE A 735 " --> pdb=" O ILE A 731 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE A 737 " --> pdb=" O PHE A 733 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN A 741 " --> pdb=" O PHE A 737 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 904 through 911 Processing helix chain 'A' and resid 914 through 918 Processing helix chain 'A' and resid 928 through 969 removed outlier: 3.866A pdb=" N LEU A 953 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 954 " --> pdb=" O ASN A 930 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN A 955 " --> pdb=" O HIS A 931 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A 956 " --> pdb=" O ILE A 952 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP A 957 " --> pdb=" O LEU A 953 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE A 968 " --> pdb=" O PHE A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1007 removed outlier: 4.846A pdb=" N GLN A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1016 No H-bonds generated for 'chain 'A' and resid 1013 through 1016' Processing helix chain 'A' and resid 1019 through 1032 Proline residue: A1025 - end of helix Processing helix chain 'A' and resid 1039 through 1071 removed outlier: 3.509A pdb=" N THR A1056 " --> pdb=" O ILE A1052 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN A1069 " --> pdb=" O CYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1121 through 1132 removed outlier: 3.637A pdb=" N SER A1132 " --> pdb=" O LEU A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1191 removed outlier: 3.781A pdb=" N TYR A1169 " --> pdb=" O PHE A1165 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ILE A1170 " --> pdb=" O PHE A1166 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N VAL A1187 " --> pdb=" O GLY A1183 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N THR A1188 " --> pdb=" O PHE A1184 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A1189 " --> pdb=" O VAL A1185 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1213 Processing helix chain 'A' and resid 1227 through 1237 removed outlier: 3.556A pdb=" N VAL A1232 " --> pdb=" O HIS A1228 " (cutoff:3.500A) Processing helix chain 'A' and resid 1239 through 1255 Processing helix chain 'A' and resid 1265 through 1292 Processing helix chain 'A' and resid 1295 through 1299 Processing helix chain 'A' and resid 1302 through 1322 Processing helix chain 'A' and resid 1375 through 1387 removed outlier: 3.798A pdb=" N PHE A1379 " --> pdb=" O PHE A1375 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG A1380 " --> pdb=" O PHE A1376 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL A1381 " --> pdb=" O ARG A1377 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET A1382 " --> pdb=" O LEU A1378 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG A1383 " --> pdb=" O PHE A1379 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU A1384 " --> pdb=" O ARG A1380 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LYS A1386 " --> pdb=" O MET A1382 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU A1387 " --> pdb=" O ARG A1383 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1375 through 1387' Processing helix chain 'A' and resid 1392 through 1404 removed outlier: 3.526A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1413 through 1429 Processing helix chain 'A' and resid 1450 through 1461 Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1498 through 1525 removed outlier: 3.622A pdb=" N ILE A1505 " --> pdb=" O PHE A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1543 through 1551 removed outlier: 3.526A pdb=" N GLU A1551 " --> pdb=" O ARG A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1567 removed outlier: 3.629A pdb=" N VAL A1566 " --> pdb=" O LEU A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1591 Processing helix chain 'A' and resid 1606 through 1617 Processing helix chain 'A' and resid 1625 through 1635 Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.739A pdb=" N MET D 40 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU D 44 " --> pdb=" O MET D 40 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR D 46 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LEU D 47 " --> pdb=" O ASP D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 58 removed outlier: 3.686A pdb=" N VAL D 58 " --> pdb=" O VAL D 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 54 through 58' Processing helix chain 'D' and resid 60 through 63 No H-bonds generated for 'chain 'D' and resid 60 through 63' Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 75 through 110 removed outlier: 3.507A pdb=" N GLU D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.693A pdb=" N ASN D 184 " --> pdb=" O LEU D 180 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 199 removed outlier: 3.569A pdb=" N ARG D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU D 199 " --> pdb=" O LYS D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 248 removed outlier: 3.690A pdb=" N GLY D 247 " --> pdb=" O TRP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 267 through 282 removed outlier: 4.094A pdb=" N GLU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 324 removed outlier: 3.529A pdb=" N LYS D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.551A pdb=" N LEU D 344 " --> pdb=" O ALA D 340 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 345 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 376 Processing helix chain 'D' and resid 397 through 405 removed outlier: 3.696A pdb=" N ALA D 403 " --> pdb=" O ILE D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 423 removed outlier: 3.526A pdb=" N THR D 423 " --> pdb=" O ILE D 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 419 through 423' Processing helix chain 'D' and resid 425 through 430 removed outlier: 3.717A pdb=" N ASP D 428 " --> pdb=" O GLU D 425 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 429 " --> pdb=" O TYR D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 441 removed outlier: 4.134A pdb=" N GLY D 438 " --> pdb=" O MET D 434 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP D 439 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LYS D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 500 removed outlier: 3.777A pdb=" N LEU D 500 " --> pdb=" O ASP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 564 No H-bonds generated for 'chain 'D' and resid 561 through 564' Processing helix chain 'D' and resid 570 through 579 Processing helix chain 'D' and resid 640 through 648 removed outlier: 4.082A pdb=" N THR D 647 " --> pdb=" O ARG D 643 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU D 648 " --> pdb=" O TYR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 removed outlier: 4.724A pdb=" N GLU D 654 " --> pdb=" O ASP D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 684 Processing helix chain 'D' and resid 700 through 718 removed outlier: 3.987A pdb=" N GLY D 710 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU D 715 " --> pdb=" O PHE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 750 removed outlier: 3.757A pdb=" N GLU D 750 " --> pdb=" O GLU D 747 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 747 through 750' Processing helix chain 'D' and resid 758 through 760 No H-bonds generated for 'chain 'D' and resid 758 through 760' Processing helix chain 'D' and resid 762 through 769 removed outlier: 3.601A pdb=" N ASP D 769 " --> pdb=" O LYS D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 818 through 826 removed outlier: 3.591A pdb=" N GLU D 823 " --> pdb=" O ASN D 819 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN D 824 " --> pdb=" O SER D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 870 Processing helix chain 'D' and resid 875 through 878 No H-bonds generated for 'chain 'D' and resid 875 through 878' Processing helix chain 'D' and resid 880 through 888 Processing helix chain 'D' and resid 1021 through 1023 No H-bonds generated for 'chain 'D' and resid 1021 through 1023' Processing helix chain 'D' and resid 1043 through 1046 No H-bonds generated for 'chain 'D' and resid 1043 through 1046' Processing sheet with id= A, first strand: chain 'A' and resid 296 through 298 removed outlier: 3.761A pdb=" N THR A 297 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS A 333 " --> pdb=" O THR A 297 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 1092 through 1096 Processing sheet with id= C, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= D, first strand: chain 'D' and resid 122 through 124 Processing sheet with id= E, first strand: chain 'D' and resid 165 through 167 removed outlier: 7.099A pdb=" N VAL D 466 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL D 487 " --> pdb=" O LEU D 464 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU D 464 " --> pdb=" O VAL D 487 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY D 489 " --> pdb=" O GLY D 462 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY D 462 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP D 491 " --> pdb=" O ILE D 460 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE D 460 " --> pdb=" O ASP D 491 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 410 through 413 removed outlier: 8.271A pdb=" N TYR D 411 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR D 386 " --> pdb=" O TYR D 411 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE D 413 " --> pdb=" O THR D 386 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER D 388 " --> pdb=" O ILE D 413 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU D 255 " --> pdb=" O MET D 359 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N PHE D 361 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU D 257 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN D 290 " --> pdb=" O ILE D 256 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 258 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA D 292 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 511 through 515 removed outlier: 3.548A pdb=" N ILE D 515 " --> pdb=" O SER D 618 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER D 618 " --> pdb=" O ILE D 515 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 732 through 736 removed outlier: 3.940A pdb=" N MET D 793 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 848 through 853 removed outlier: 3.692A pdb=" N MET D1017 " --> pdb=" O HIS D1004 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU D1019 " --> pdb=" O ILE D1002 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE D1002 " --> pdb=" O GLU D1019 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 892 through 899 removed outlier: 3.606A pdb=" N GLN D 980 " --> pdb=" O ASN D 895 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 976 " --> pdb=" O ASP D 899 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE D 975 " --> pdb=" O SER D1038 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 902 through 904 removed outlier: 3.812A pdb=" N SER D 902 " --> pdb=" O CYS D 974 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 1968 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.60 Time building geometry restraints manager: 8.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 4326 1.33 - 1.48: 5584 1.48 - 1.63: 7502 1.63 - 1.78: 2 1.78 - 1.92: 138 Bond restraints: 17552 Sorted by residual: bond pdb=" C03 WB9 A2303 " pdb=" C08 WB9 A2303 " ideal model delta sigma weight residual 1.226 1.501 -0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" CA ASP A 311 " pdb=" C ASP A 311 " ideal model delta sigma weight residual 1.524 1.467 0.057 7.00e-03 2.04e+04 6.68e+01 bond pdb=" C07 WB9 A2303 " pdb=" C08 WB9 A2303 " ideal model delta sigma weight residual 1.348 1.510 -0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" CA PRO A 146 " pdb=" CB PRO A 146 " ideal model delta sigma weight residual 1.535 1.447 0.088 1.12e-02 7.97e+03 6.13e+01 bond pdb=" CA CYS A 316 " pdb=" C CYS A 316 " ideal model delta sigma weight residual 1.524 1.438 0.086 1.24e-02 6.50e+03 4.81e+01 ... (remaining 17547 not shown) Histogram of bond angle deviations from ideal: 66.33 - 80.79: 5 80.79 - 95.25: 4 95.25 - 109.70: 2410 109.70 - 124.16: 21083 124.16 - 138.62: 320 Bond angle restraints: 23822 Sorted by residual: angle pdb=" C01 WB9 A2303 " pdb=" C02 WB9 A2303 " pdb=" C32 WB9 A2303 " ideal model delta sigma weight residual 115.48 74.81 40.67 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C02 WB9 A2303 " pdb=" C03 WB9 A2303 " pdb=" C04 WB9 A2303 " ideal model delta sigma weight residual 105.14 66.33 38.81 3.00e+00 1.11e-01 1.67e+02 angle pdb=" C02 WB9 A2303 " pdb=" C07 WB9 A2303 " pdb=" C06 WB9 A2303 " ideal model delta sigma weight residual 105.92 67.13 38.79 3.00e+00 1.11e-01 1.67e+02 angle pdb=" N ALA A1032 " pdb=" CA ALA A1032 " pdb=" C ALA A1032 " ideal model delta sigma weight residual 113.21 99.40 13.81 1.15e+00 7.56e-01 1.44e+02 angle pdb=" C01 WB9 A2303 " pdb=" C02 WB9 A2303 " pdb=" C03 WB9 A2303 " ideal model delta sigma weight residual 113.78 78.74 35.04 3.00e+00 1.11e-01 1.36e+02 ... (remaining 23817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.72: 9890 27.72 - 55.43: 673 55.43 - 83.15: 103 83.15 - 110.87: 44 110.87 - 138.59: 6 Dihedral angle restraints: 10716 sinusoidal: 4423 harmonic: 6293 Sorted by residual: dihedral pdb=" CB CYS D 904 " pdb=" SG CYS D 904 " pdb=" SG CYS D 974 " pdb=" CB CYS D 974 " ideal model delta sinusoidal sigma weight residual 93.00 174.29 -81.29 1 1.00e+01 1.00e-02 8.15e+01 dihedral pdb=" CB CYS A 316 " pdb=" SG CYS A 316 " pdb=" SG CYS A 332 " pdb=" CB CYS A 332 " ideal model delta sinusoidal sigma weight residual -86.00 -148.84 62.84 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS A 298 " pdb=" SG CYS A 298 " pdb=" SG CYS A 326 " pdb=" CB CYS A 326 " ideal model delta sinusoidal sigma weight residual -86.00 -140.31 54.31 1 1.00e+01 1.00e-02 4.00e+01 ... (remaining 10713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.932: 2760 0.932 - 1.865: 0 1.865 - 2.797: 0 2.797 - 3.729: 0 3.729 - 4.662: 1 Chirality restraints: 2761 Sorted by residual: chirality pdb=" N14 WB9 A2303 " pdb=" C15 WB9 A2303 " pdb=" C19 WB9 A2303 " pdb=" C20 WB9 A2303 " both_signs ideal model delta sigma weight residual False 2.35 -2.32 4.66 2.00e-01 2.50e+01 5.43e+02 chirality pdb=" C1 NAG E 3 " pdb=" O4 NAG E 2 " pdb=" C2 NAG E 3 " pdb=" O5 NAG E 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.38e+02 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.12e+02 ... (remaining 2758 not shown) Planarity restraints: 3005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 4 " -0.339 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 4 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 4 " -0.153 2.00e-02 2.50e+03 pdb=" N2 NAG E 4 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG E 4 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 3 " -0.321 2.00e-02 2.50e+03 2.71e-01 9.15e+02 pdb=" C7 NAG E 3 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 3 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG E 3 " 0.468 2.00e-02 2.50e+03 pdb=" O7 NAG E 3 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.103 2.00e-02 2.50e+03 8.30e-02 8.62e+01 pdb=" C7 NAG E 2 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.129 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.025 2.00e-02 2.50e+03 ... (remaining 3002 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 194 2.52 - 3.12: 14905 3.12 - 3.71: 26976 3.71 - 4.31: 38305 4.31 - 4.90: 60252 Nonbonded interactions: 140632 Sorted by model distance: nonbonded pdb=" NH2 ARG A 511 " pdb=" CE2 PHE A 512 " model vdw 1.927 3.420 nonbonded pdb=" CZ ARG A 511 " pdb=" CE2 PHE A 512 " model vdw 1.966 3.570 nonbonded pdb=" OH TYR D 788 " pdb=" O THR D 868 " model vdw 2.197 2.440 nonbonded pdb=" O4 NAG C 2 " pdb=" O7 NAG C 2 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR D 599 " pdb=" OD2 ASP D 854 " model vdw 2.203 2.440 ... (remaining 140627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } 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 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.600 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 50.620 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 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 : 0.009 0.275 17552 Z= 0.570 Angle : 1.288 40.671 23822 Z= 0.774 Chirality : 0.108 4.662 2761 Planarity : 0.009 0.291 2998 Dihedral : 19.613 138.585 6612 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 29.12 Ramachandran Plot: Outliers : 1.70 % Allowed : 9.40 % Favored : 88.89 % Rotamer: Outliers : 5.51 % Allowed : 23.80 % Favored : 70.69 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.56 % 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: -2.74 (0.17), residues: 2116 helix: -1.30 (0.15), residues: 1042 sheet: -0.95 (0.38), residues: 190 loop : -2.59 (0.19), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 336 HIS 0.004 0.001 HIS A1540 PHE 0.024 0.001 PHE D 686 TYR 0.025 0.001 TYR A 144 ARG 0.013 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 474 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 29 residues processed: 542 average time/residue: 0.3186 time to fit residues: 256.2477 Evaluate side-chains 331 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 302 time to evaluate : 1.979 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1901 time to fit residues: 12.2701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 0.4980 chunk 64 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 259 ASN A 341 HIS A 510 ASN A 556 GLN A 560 ASN ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 GLN A 955 ASN A1103 HIS A1113 ASN A1157 ASN A1205 ASN A1252 ASN A1259 GLN A1452 GLN D 77 GLN D 314 ASN D 324 ASN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 ASN D 652 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1004 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17552 Z= 0.269 Angle : 0.923 33.100 23822 Z= 0.423 Chirality : 0.063 2.146 2761 Planarity : 0.006 0.084 2998 Dihedral : 14.182 150.087 2738 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.05 % Favored : 93.67 % Rotamer: Outliers : 4.62 % Allowed : 25.58 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.57 (0.18), residues: 2116 helix: -0.26 (0.16), residues: 1042 sheet: -0.96 (0.36), residues: 205 loop : -1.97 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 382 HIS 0.007 0.001 HIS A1260 PHE 0.047 0.002 PHE A 909 TYR 0.040 0.002 TYR A1169 ARG 0.007 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 313 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 34 residues processed: 369 average time/residue: 0.2829 time to fit residues: 160.8768 Evaluate side-chains 299 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 265 time to evaluate : 2.024 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.2229 time to fit residues: 15.1480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 194 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 66 optimal weight: 20.0000 chunk 156 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN A 694 GLN A1252 ASN ** A1573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN D 324 ASN D 374 ASN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 595 GLN D 753 GLN D 885 HIS ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17552 Z= 0.246 Angle : 0.862 31.412 23822 Z= 0.383 Chirality : 0.060 2.090 2761 Planarity : 0.005 0.078 2998 Dihedral : 12.031 159.193 2738 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 3.17 % Allowed : 25.92 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.10 (0.18), residues: 2116 helix: 0.24 (0.16), residues: 1026 sheet: -0.91 (0.35), residues: 205 loop : -1.83 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 336 HIS 0.009 0.001 HIS A1260 PHE 0.042 0.002 PHE A 909 TYR 0.019 0.001 TYR A 713 ARG 0.013 0.000 ARG A1559 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 286 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 19 residues processed: 326 average time/residue: 0.2882 time to fit residues: 146.3851 Evaluate side-chains 272 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 253 time to evaluate : 1.970 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1699 time to fit residues: 8.6572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 3.9990 chunk 146 optimal weight: 0.0770 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 195 optimal weight: 0.5980 chunk 206 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN D 374 ASN D 406 ASN ** D 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17552 Z= 0.201 Angle : 0.810 31.144 23822 Z= 0.356 Chirality : 0.058 2.080 2761 Planarity : 0.005 0.086 2998 Dihedral : 11.216 163.082 2738 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer: Outliers : 2.78 % Allowed : 25.47 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.89 (0.18), residues: 2116 helix: 0.45 (0.16), residues: 1032 sheet: -0.83 (0.35), residues: 205 loop : -1.78 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 185 HIS 0.008 0.001 HIS A1260 PHE 0.037 0.002 PHE A1405 TYR 0.038 0.001 TYR A 299 ARG 0.010 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 270 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 24 residues processed: 302 average time/residue: 0.2704 time to fit residues: 130.4310 Evaluate side-chains 270 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 246 time to evaluate : 1.972 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 24 outliers final: 1 residues processed: 24 average time/residue: 0.1650 time to fit residues: 10.1173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 105 optimal weight: 0.4980 chunk 185 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 GLN ** A 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1060 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 HIS D 246 GLN D 374 ASN D 406 ASN D 526 ASN D 641 GLN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17552 Z= 0.288 Angle : 0.845 31.439 23822 Z= 0.376 Chirality : 0.058 1.984 2761 Planarity : 0.005 0.090 2998 Dihedral : 10.701 165.533 2738 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.19 % Favored : 93.71 % Rotamer: Outliers : 2.89 % Allowed : 26.03 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.91 (0.18), residues: 2116 helix: 0.45 (0.16), residues: 1035 sheet: -0.81 (0.36), residues: 193 loop : -1.82 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.005 0.001 HIS A1260 PHE 0.021 0.002 PHE D 686 TYR 0.034 0.002 TYR A1169 ARG 0.011 0.001 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 274 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 27 residues processed: 305 average time/residue: 0.2728 time to fit residues: 128.6715 Evaluate side-chains 267 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 1.991 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.1644 time to fit residues: 11.1416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 50.0000 chunk 186 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1252 ASN ** A1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 HIS D 374 ASN D 604 ASN D 682 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1033 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.6333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 17552 Z= 0.425 Angle : 0.897 31.766 23822 Z= 0.409 Chirality : 0.061 2.015 2761 Planarity : 0.005 0.085 2998 Dihedral : 10.656 164.423 2738 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.19 % Rotamer: Outliers : 3.00 % Allowed : 26.75 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.18 (0.18), residues: 2116 helix: 0.27 (0.16), residues: 1063 sheet: -1.02 (0.35), residues: 200 loop : -2.08 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 336 HIS 0.004 0.001 HIS D 392 PHE 0.017 0.002 PHE D 825 TYR 0.040 0.002 TYR A 299 ARG 0.008 0.001 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 273 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 27 residues processed: 311 average time/residue: 0.2922 time to fit residues: 139.1054 Evaluate side-chains 264 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 237 time to evaluate : 1.853 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 27 outliers final: 1 residues processed: 27 average time/residue: 0.1567 time to fit residues: 10.4125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 8.9990 chunk 23 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 20.0000 chunk 206 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1259 GLN D 246 GLN D 481 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17552 Z= 0.204 Angle : 0.828 31.124 23822 Z= 0.363 Chirality : 0.058 2.029 2761 Planarity : 0.005 0.086 2998 Dihedral : 9.703 166.404 2738 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.33 % Allowed : 27.59 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.84 (0.18), residues: 2116 helix: 0.56 (0.16), residues: 1052 sheet: -1.06 (0.34), residues: 212 loop : -1.85 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 185 HIS 0.003 0.001 HIS D 885 PHE 0.021 0.002 PHE D1003 TYR 0.023 0.001 TYR A1503 ARG 0.011 0.000 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 265 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 279 average time/residue: 0.2835 time to fit residues: 123.3588 Evaluate side-chains 254 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 243 time to evaluate : 1.963 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.2049 time to fit residues: 6.5017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 19 optimal weight: 10.0000 chunk 162 optimal weight: 0.6980 chunk 187 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 ASN D 374 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.6696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17552 Z= 0.205 Angle : 0.815 31.242 23822 Z= 0.359 Chirality : 0.057 2.037 2761 Planarity : 0.005 0.080 2998 Dihedral : 9.044 171.201 2738 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.22 % Allowed : 28.14 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.72 (0.18), residues: 2116 helix: 0.65 (0.16), residues: 1058 sheet: -0.96 (0.36), residues: 199 loop : -1.79 (0.21), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1641 HIS 0.002 0.001 HIS D 306 PHE 0.021 0.002 PHE A 532 TYR 0.020 0.001 TYR A1503 ARG 0.008 0.000 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 255 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 267 average time/residue: 0.2796 time to fit residues: 115.7833 Evaluate side-chains 254 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 241 time to evaluate : 2.003 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.1664 time to fit residues: 6.9609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 chunk 192 optimal weight: 0.0770 chunk 115 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 overall best weight: 2.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 ASN A1446 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.7021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17552 Z= 0.380 Angle : 0.873 31.296 23822 Z= 0.395 Chirality : 0.060 2.021 2761 Planarity : 0.005 0.083 2998 Dihedral : 9.003 169.427 2738 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.06 % Allowed : 28.53 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.91 (0.18), residues: 2116 helix: 0.55 (0.16), residues: 1051 sheet: -1.12 (0.35), residues: 197 loop : -1.92 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 380 HIS 0.004 0.001 HIS D 167 PHE 0.027 0.002 PHE D 686 TYR 0.020 0.002 TYR A1169 ARG 0.008 0.001 ARG A1383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 272 average time/residue: 0.2908 time to fit residues: 122.3924 Evaluate side-chains 253 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 242 time to evaluate : 2.204 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 11 outliers final: 1 residues processed: 11 average time/residue: 0.1891 time to fit residues: 6.6349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.7151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17552 Z= 0.237 Angle : 0.832 34.356 23822 Z= 0.371 Chirality : 0.058 2.019 2761 Planarity : 0.005 0.083 2998 Dihedral : 8.781 169.504 2738 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.44 % Allowed : 29.48 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.77 (0.18), residues: 2116 helix: 0.63 (0.16), residues: 1054 sheet: -1.06 (0.35), residues: 199 loop : -1.81 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1641 HIS 0.002 0.001 HIS D 392 PHE 0.030 0.002 PHE D 686 TYR 0.023 0.001 TYR D 644 ARG 0.007 0.000 ARG A1547 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4232 Ramachandran restraints generated. 2116 Oldfield, 0 Emsley, 2116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 253 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 257 average time/residue: 0.2870 time to fit residues: 114.9569 Evaluate side-chains 246 residues out of total 1907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 241 time to evaluate : 2.201 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.1707 time to fit residues: 4.2876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 174 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 30.0000 chunk 149 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 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 120 ASN D 753 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1012 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1033 GLN ** 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 = 0.4357 r_free = 0.4357 target = 0.203909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.150280 restraints weight = 22347.221| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.59 r_work: 0.3301 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.7243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17552 Z= 0.209 Angle : 0.836 32.107 23822 Z= 0.371 Chirality : 0.058 2.032 2761 Planarity : 0.005 0.082 2998 Dihedral : 8.650 172.213 2738 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.44 % Allowed : 29.87 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: -0.66 (0.18), residues: 2116 helix: 0.70 (0.16), residues: 1057 sheet: -0.96 (0.36), residues: 199 loop : -1.74 (0.21), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1641 HIS 0.002 0.000 HIS D 306 PHE 0.031 0.001 PHE D 686 TYR 0.025 0.001 TYR A1169 ARG 0.008 0.000 ARG D 643 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4088.46 seconds wall clock time: 74 minutes 47.45 seconds (4487.45 seconds total)