Starting phenix.real_space_refine on Thu Feb 15 08:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pem_13353/02_2024/7pem_13353_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pem_13353/02_2024/7pem_13353.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pem_13353/02_2024/7pem_13353_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pem_13353/02_2024/7pem_13353_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pem_13353/02_2024/7pem_13353_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pem_13353/02_2024/7pem_13353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pem_13353/02_2024/7pem_13353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pem_13353/02_2024/7pem_13353_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pem_13353/02_2024/7pem_13353_updated.pdb" } resolution = 3.1 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= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 7504 2.51 5 N 1865 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ARG 309": "NH1" <-> "NH2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A ASP 398": "OD1" <-> "OD2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A TYR 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 515": "OE1" <-> "OE2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A ASP 537": "OD1" <-> "OD2" Residue "A TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 584": "OD1" <-> "OD2" Residue "A ASP 589": "OD1" <-> "OD2" Residue "A GLU 599": "OE1" <-> "OE2" Residue "A TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ASP 619": "OD1" <-> "OD2" Residue "A ASP 625": "OD1" <-> "OD2" Residue "A PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A ASP 654": "OD1" <-> "OD2" Residue "A GLU 655": "OE1" <-> "OE2" Residue "A GLU 683": "OE1" <-> "OE2" Residue "A GLU 687": "OE1" <-> "OE2" Residue "A PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 729": "OE1" <-> "OE2" Residue "A ARG 730": "NH1" <-> "NH2" Residue "A ASP 732": "OD1" <-> "OD2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 762": "NH1" <-> "NH2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 788": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A ASP 811": "OD1" <-> "OD2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A GLU 840": "OE1" <-> "OE2" Residue "A ARG 850": "NH1" <-> "NH2" Residue "A GLU 854": "OE1" <-> "OE2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ASP 868": "OD1" <-> "OD2" Residue "A GLU 870": "OE1" <-> "OE2" Residue "A ARG 871": "NH1" <-> "NH2" Residue "A GLU 875": "OE1" <-> "OE2" Residue "A ASP 889": "OD1" <-> "OD2" Residue "A ASP 898": "OD1" <-> "OD2" Residue "A ARG 928": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ASP 954": "OD1" <-> "OD2" Residue "A ASP 958": "OD1" <-> "OD2" Residue "A PHE 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1071": "NH1" <-> "NH2" Residue "A TYR 1080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1191": "OE1" <-> "OE2" Residue "A TYR 1192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1219": "NH1" <-> "NH2" Residue "A TYR 1225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 90": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C ARG 112": "NH1" <-> "NH2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C ASP 158": "OD1" <-> "OD2" Residue "C ASP 171": "OD1" <-> "OD2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "C ASP 227": "OD1" <-> "OD2" Residue "C ARG 228": "NH1" <-> "NH2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ARG 359": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11620 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1066, 8522 Classifications: {'peptide': 1066} Link IDs: {'PTRANS': 30, 'TRANS': 1035} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2841 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 21, 'TRANS': 328} Chain: "B" 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: "D" 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 2, 'NAG': 2} 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: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 151 Unusual residues: {' MG': 1, '2Y5': 1, 'ATP': 1, 'Q3G': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 6.60, per 1000 atoms: 0.57 Number of scatterers: 11620 At special positions: 0 Unit cell: (88.6832, 105.182, 178.398, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 7 15.00 Mg 1 11.99 O 2195 8.00 N 1865 7.00 C 7504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 190 " distance=2.04 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 Atom "HETATM11403 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " BMA E 3 " - " BMA E 4 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG B 1 " - " ASN C 288 " " NAG D 1 " - " ASN C 216 " " NAG E 1 " - " ASN C 199 " Time building additional restraints: 5.03 Conformation dependent library (CDL) restraints added in 2.3 seconds 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 11 sheets defined 36.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 193 through 196 Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 251 through 278 removed outlier: 3.962A pdb=" N GLU A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 439 through 474 removed outlier: 3.592A pdb=" N ARG A 446 " --> pdb=" O LYS A 442 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 449 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 501 removed outlier: 3.615A pdb=" N PHE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 508 through 527 removed outlier: 3.819A pdb=" N VAL A 512 " --> pdb=" O ILE A 508 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 525 " --> pdb=" O GLN A 521 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 526 " --> pdb=" O ALA A 522 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 527 " --> pdb=" O PHE A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 549 through 552 removed outlier: 4.114A pdb=" N GLY A 552 " --> pdb=" O GLU A 549 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 549 through 552' Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 620 through 631 Processing helix chain 'A' and resid 653 through 665 Processing helix chain 'A' and resid 728 through 730 No H-bonds generated for 'chain 'A' and resid 728 through 730' Processing helix chain 'A' and resid 740 through 750 Processing helix chain 'A' and resid 769 through 780 removed outlier: 4.606A pdb=" N SER A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ALA A 780 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 794 removed outlier: 3.899A pdb=" N ALA A 794 " --> pdb=" O LEU A 790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 790 through 794' Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 839 through 844 removed outlier: 3.659A pdb=" N ASN A 844 " --> pdb=" O GLU A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 881 Processing helix chain 'A' and resid 899 through 905 Processing helix chain 'A' and resid 912 through 920 removed outlier: 3.742A pdb=" N VAL A 917 " --> pdb=" O TYR A 913 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS A 919 " --> pdb=" O LEU A 915 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU A 920 " --> pdb=" O THR A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 943 removed outlier: 4.076A pdb=" N ALA A 935 " --> pdb=" O PRO A 931 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 938 " --> pdb=" O LYS A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 962 removed outlier: 4.087A pdb=" N VAL A 959 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N SER A 960 " --> pdb=" O ASN A 957 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET A 961 " --> pdb=" O ASP A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 981 No H-bonds generated for 'chain 'A' and resid 978 through 981' Processing helix chain 'A' and resid 991 through 998 removed outlier: 3.778A pdb=" N LEU A 996 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 997 " --> pdb=" O LYS A 994 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 998 " --> pdb=" O LYS A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1018 removed outlier: 3.769A pdb=" N SER A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1023 No H-bonds generated for 'chain 'A' and resid 1020 through 1023' Processing helix chain 'A' and resid 1025 through 1028 No H-bonds generated for 'chain 'A' and resid 1025 through 1028' Processing helix chain 'A' and resid 1030 through 1032 No H-bonds generated for 'chain 'A' and resid 1030 through 1032' Processing helix chain 'A' and resid 1043 through 1047 Processing helix chain 'A' and resid 1049 through 1052 No H-bonds generated for 'chain 'A' and resid 1049 through 1052' Processing helix chain 'A' and resid 1056 through 1062 Processing helix chain 'A' and resid 1070 through 1073 No H-bonds generated for 'chain 'A' and resid 1070 through 1073' Processing helix chain 'A' and resid 1077 through 1084 Processing helix chain 'A' and resid 1091 through 1115 removed outlier: 3.626A pdb=" N GLY A1096 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TRP A1097 " --> pdb=" O ILE A1093 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A1100 " --> pdb=" O GLY A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1153 removed outlier: 4.252A pdb=" N THR A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A1146 " --> pdb=" O SER A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1166 through 1182 removed outlier: 3.601A pdb=" N LEU A1170 " --> pdb=" O PRO A1166 " (cutoff:3.500A) Proline residue: A1177 - end of helix removed outlier: 3.533A pdb=" N SER A1181 " --> pdb=" O PRO A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1186 No H-bonds generated for 'chain 'A' and resid 1184 through 1186' Processing helix chain 'A' and resid 1195 through 1199 Processing helix chain 'A' and resid 1204 through 1216 removed outlier: 3.898A pdb=" N LEU A1209 " --> pdb=" O PHE A1205 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A1210 " --> pdb=" O TRP A1206 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A1211 " --> pdb=" O LEU A1207 " (cutoff:3.500A) Proline residue: A1213 - end of helix Processing helix chain 'A' and resid 1218 through 1229 removed outlier: 3.693A pdb=" N LEU A1222 " --> pdb=" O VAL A1218 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A1225 " --> pdb=" O PHE A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1244 removed outlier: 3.797A pdb=" N ILE A1238 " --> pdb=" O THR A1234 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 67 removed outlier: 3.838A pdb=" N LEU C 46 " --> pdb=" O PRO C 42 " (cutoff:3.500A) Proline residue: C 47 - end of helix Proline residue: C 58 - end of helix removed outlier: 3.698A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 83 No H-bonds generated for 'chain 'C' and resid 80 through 83' Processing helix chain 'C' and resid 94 through 96 No H-bonds generated for 'chain 'C' and resid 94 through 96' Processing helix chain 'C' and resid 151 through 154 No H-bonds generated for 'chain 'C' and resid 151 through 154' Processing helix chain 'C' and resid 227 through 230 No H-bonds generated for 'chain 'C' and resid 227 through 230' Processing helix chain 'C' and resid 245 through 247 No H-bonds generated for 'chain 'C' and resid 245 through 247' Processing helix chain 'C' and resid 267 through 273 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 331 through 343 removed outlier: 3.995A pdb=" N LEU C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 352 through 355 No H-bonds generated for 'chain 'C' and resid 352 through 355' Processing sheet with id= A, first strand: chain 'A' and resid 183 through 186 Processing sheet with id= B, first strand: chain 'A' and resid 283 through 288 removed outlier: 3.744A pdb=" N SER A 288 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP A 293 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 307 through 310 removed outlier: 6.989A pdb=" N ASP A 319 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 346 through 349 removed outlier: 3.966A pdb=" N TYR A 333 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 894 through 897 removed outlier: 6.779A pdb=" N ALA A 923 " --> pdb=" O LEU A 895 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE A 897 " --> pdb=" O ALA A 923 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE A 925 " --> pdb=" O ILE A 897 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL A 924 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU A 948 " --> pdb=" O GLU A 555 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE A 557 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU A 950 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER A 559 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE A 952 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 967 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N GLY A 953 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 969 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 985 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 570 through 572 removed outlier: 6.898A pdb=" N LEU A 759 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ALA A 806 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU A 757 " --> pdb=" O ALA A 806 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA A 808 " --> pdb=" O ARG A 755 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG A 755 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 716 " --> pdb=" O ILE A 764 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER A 706 " --> pdb=" O CYS A 696 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ARG A 710 " --> pdb=" O LEU A 692 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 692 " --> pdb=" O ARG A 710 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 580 through 583 Processing sheet with id= H, first strand: chain 'A' and resid 637 through 640 Processing sheet with id= I, first strand: chain 'A' and resid 667 through 673 removed outlier: 6.705A pdb=" N THR A 678 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG A 672 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 97 through 100 removed outlier: 6.636A pdb=" N TYR C 141 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU C 284 " --> pdb=" O TYR C 141 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE C 143 " --> pdb=" O TYR C 282 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR C 282 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 110 through 115 355 hydrogen bonds defined for protein. 1002 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: 4.25 Time building geometry restraints manager: 5.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1924 1.32 - 1.46: 4556 1.46 - 1.60: 5317 1.60 - 1.74: 5 1.74 - 1.88: 81 Bond restraints: 11883 Sorted by residual: bond pdb=" O5' ATP A1403 " pdb=" PA ATP A1403 " ideal model delta sigma weight residual 1.579 1.882 -0.303 1.10e-02 8.26e+03 7.61e+02 bond pdb=" O3A ATP A1403 " pdb=" PB ATP A1403 " ideal model delta sigma weight residual 1.592 1.829 -0.237 1.10e-02 8.26e+03 4.66e+02 bond pdb=" C5' ATP A1403 " pdb=" O5' ATP A1403 " ideal model delta sigma weight residual 1.443 1.341 0.102 1.00e-02 1.00e+04 1.04e+02 bond pdb=" O3B ATP A1403 " pdb=" PG ATP A1403 " ideal model delta sigma weight residual 1.600 1.758 -0.158 2.80e-02 1.28e+03 3.18e+01 bond pdb=" C2 ATP A1403 " pdb=" N1 ATP A1403 " ideal model delta sigma weight residual 1.334 1.378 -0.044 1.00e-02 1.00e+04 1.91e+01 ... (remaining 11878 not shown) Histogram of bond angle deviations from ideal: 88.56 - 97.66: 6 97.66 - 106.76: 305 106.76 - 115.86: 7528 115.86 - 124.96: 8091 124.96 - 134.07: 177 Bond angle restraints: 16107 Sorted by residual: angle pdb=" PA ATP A1403 " pdb=" O3A ATP A1403 " pdb=" PB ATP A1403 " ideal model delta sigma weight residual 136.83 109.76 27.07 1.00e+00 1.00e+00 7.33e+02 angle pdb=" PB ATP A1403 " pdb=" O3B ATP A1403 " pdb=" PG ATP A1403 " ideal model delta sigma weight residual 139.87 113.20 26.67 1.00e+00 1.00e+00 7.11e+02 angle pdb=" C5' ATP A1403 " pdb=" O5' ATP A1403 " pdb=" PA ATP A1403 " ideal model delta sigma weight residual 121.27 105.44 15.83 1.00e+00 1.00e+00 2.51e+02 angle pdb=" C21 2Y5 A1401 " pdb=" C22 2Y5 A1401 " pdb=" C23 2Y5 A1401 " ideal model delta sigma weight residual 85.82 120.50 -34.68 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C18 2Y5 A1401 " pdb=" C19 2Y5 A1401 " pdb=" C20 2Y5 A1401 " ideal model delta sigma weight residual 152.65 119.69 32.96 3.00e+00 1.11e-01 1.21e+02 ... (remaining 16102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 6860 33.14 - 66.28: 298 66.28 - 99.42: 35 99.42 - 132.56: 10 132.56 - 165.70: 3 Dihedral angle restraints: 7206 sinusoidal: 3050 harmonic: 4156 Sorted by residual: dihedral pdb=" CB CYS C 176 " pdb=" SG CYS C 176 " pdb=" SG CYS C 190 " pdb=" CB CYS C 190 " ideal model delta sinusoidal sigma weight residual 93.00 35.20 57.80 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" C24 2Y5 A1401 " pdb=" C25 2Y5 A1401 " pdb=" C26 2Y5 A1401 " pdb=" C27 2Y5 A1401 " ideal model delta sinusoidal sigma weight residual 329.24 163.54 165.70 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" C1 2Y5 A1401 " pdb=" O1 2Y5 A1401 " pdb=" P1 2Y5 A1401 " pdb=" O13 2Y5 A1401 " ideal model delta sinusoidal sigma weight residual 64.28 -77.17 141.45 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 7203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.694: 1838 0.694 - 1.389: 0 1.389 - 2.083: 0 2.083 - 2.778: 0 2.778 - 3.472: 1 Chirality restraints: 1839 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN C 288 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 1.07 -3.47 2.00e-01 2.50e+01 3.01e+02 chirality pdb=" C4' ATP A1403 " pdb=" C3' ATP A1403 " pdb=" C5' ATP A1403 " pdb=" O4' ATP A1403 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1836 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 216 " 0.173 2.00e-02 2.50e+03 1.84e-01 4.23e+02 pdb=" CG ASN C 216 " -0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN C 216 " -0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN C 216 " -0.277 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " 0.233 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 288 " -0.145 2.00e-02 2.50e+03 1.59e-01 3.16e+02 pdb=" CG ASN C 288 " 0.057 2.00e-02 2.50e+03 pdb=" OD1 ASN C 288 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN C 288 " 0.252 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.194 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A1056 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.32e+00 pdb=" N PRO A1057 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1057 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A1057 " 0.025 5.00e-02 4.00e+02 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 141 2.64 - 3.20: 10138 3.20 - 3.77: 17040 3.77 - 4.33: 24760 4.33 - 4.90: 40324 Nonbonded interactions: 92403 Sorted by model distance: nonbonded pdb="MG MG A1402 " pdb=" O HOH A1501 " model vdw 2.071 2.170 nonbonded pdb=" O THR A 562 " pdb="MG MG A1402 " model vdw 2.125 2.170 nonbonded pdb=" OD2 ASP C 173 " pdb=" OG SER C 175 " model vdw 2.251 2.440 nonbonded pdb=" OG1 THR A 782 " pdb=" OD1 ASP A 784 " model vdw 2.263 2.440 nonbonded pdb=" O PRO A1177 " pdb=" OG SER A1181 " model vdw 2.284 2.440 ... (remaining 92398 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 'B' selection = chain 'D' } 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: 0.690 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: 4.170 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.700 Find NCS groups from input model: 0.300 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.005 0.303 11883 Z= 0.293 Angle : 0.916 34.678 16107 Z= 0.503 Chirality : 0.091 3.472 1839 Planarity : 0.003 0.046 1999 Dihedral : 18.639 165.699 4520 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 6.06 % Allowed : 21.29 % Favored : 72.65 % 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: -3.75 (0.19), residues: 1409 helix: -2.34 (0.19), residues: 554 sheet: -1.22 (0.35), residues: 215 loop : -3.06 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1028 HIS 0.004 0.000 HIS A 745 PHE 0.015 0.001 PHE A 213 TYR 0.016 0.001 TYR A1225 ARG 0.009 0.000 ARG A 710 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 143 time to evaluate : 1.389 Fit side-chains revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7239 (mp) REVERT: A 349 GLN cc_start: 0.7632 (pt0) cc_final: 0.7267 (pt0) REVERT: A 838 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7368 (mtp180) REVERT: A 977 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6231 (mtp) REVERT: A 1178 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7594 (mt) REVERT: A 1193 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.5474 (t80) REVERT: C 121 GLN cc_start: 0.7924 (mt0) cc_final: 0.7589 (mt0) REVERT: C 250 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7978 (tttm) REVERT: C 251 TYR cc_start: 0.8790 (m-10) cc_final: 0.8571 (m-80) REVERT: C 361 MET cc_start: 0.4589 (OUTLIER) cc_final: 0.3770 (ppp) REVERT: C 366 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7311 (t80) outliers start: 76 outliers final: 48 residues processed: 209 average time/residue: 0.2161 time to fit residues: 67.3407 Evaluate side-chains 182 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 127 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 435 ILE Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 515 GLU Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 559 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 729 GLU Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 947 SER Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1090 SER Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1189 SER Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 181 SER Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 119 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 57 optimal weight: 0.0570 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 GLN A 521 GLN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 11883 Z= 0.373 Angle : 0.648 14.034 16107 Z= 0.320 Chirality : 0.047 0.183 1839 Planarity : 0.004 0.047 1999 Dihedral : 13.333 164.678 1900 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 6.06 % Allowed : 20.65 % Favored : 73.29 % 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: -2.94 (0.20), residues: 1409 helix: -1.50 (0.21), residues: 562 sheet: -0.79 (0.34), residues: 215 loop : -2.78 (0.21), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1157 HIS 0.011 0.001 HIS A1198 PHE 0.018 0.002 PHE C 269 TYR 0.022 0.002 TYR C 77 ARG 0.004 0.001 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 126 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6368 (t0) cc_final: 0.5685 (t0) REVERT: A 203 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7309 (mp) REVERT: A 349 GLN cc_start: 0.7692 (pt0) cc_final: 0.7325 (pt0) REVERT: A 549 GLU cc_start: 0.7557 (pm20) cc_final: 0.6866 (pm20) REVERT: A 674 PRO cc_start: 0.8294 (Cg_exo) cc_final: 0.8089 (Cg_endo) REVERT: A 977 MET cc_start: 0.6997 (ttm) cc_final: 0.6786 (mtp) REVERT: A 1178 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7341 (mp) REVERT: A 1193 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.6947 (t80) REVERT: A 1224 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7654 (tttp) REVERT: C 121 GLN cc_start: 0.7972 (mt0) cc_final: 0.7724 (mt0) REVERT: C 250 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8154 (ttmm) REVERT: C 251 TYR cc_start: 0.8997 (m-10) cc_final: 0.8747 (m-80) REVERT: C 361 MET cc_start: 0.4862 (ptt) cc_final: 0.4111 (ppp) REVERT: C 366 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.7226 (t80) outliers start: 76 outliers final: 53 residues processed: 191 average time/residue: 0.2056 time to fit residues: 59.8550 Evaluate side-chains 178 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 119 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain A residue 817 VAL Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1182 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1224 LYS Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 71 optimal weight: 0.0060 chunk 39 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 43 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11883 Z= 0.154 Angle : 0.521 13.086 16107 Z= 0.254 Chirality : 0.042 0.153 1839 Planarity : 0.003 0.040 1999 Dihedral : 11.823 171.390 1851 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.91 % Allowed : 23.37 % Favored : 72.73 % 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: -2.25 (0.21), residues: 1409 helix: -0.83 (0.22), residues: 553 sheet: -0.53 (0.35), residues: 221 loop : -2.45 (0.22), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1223 HIS 0.004 0.001 HIS A1198 PHE 0.018 0.001 PHE A 626 TYR 0.015 0.001 TYR C 77 ARG 0.003 0.000 ARG A 744 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 128 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6370 (t0) cc_final: 0.5648 (t0) REVERT: A 203 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7255 (mp) REVERT: A 349 GLN cc_start: 0.7662 (pt0) cc_final: 0.7297 (pt0) REVERT: A 374 GLN cc_start: 0.7936 (mm-40) cc_final: 0.7465 (mm-40) REVERT: A 598 ILE cc_start: 0.4153 (OUTLIER) cc_final: 0.3929 (mt) REVERT: A 1193 TYR cc_start: 0.7818 (OUTLIER) cc_final: 0.6695 (t80) REVERT: C 121 GLN cc_start: 0.7930 (mt0) cc_final: 0.7695 (mt0) REVERT: C 250 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8112 (ttmm) REVERT: C 361 MET cc_start: 0.4837 (ptt) cc_final: 0.4093 (ppp) REVERT: C 366 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7322 (t80) outliers start: 49 outliers final: 32 residues processed: 167 average time/residue: 0.2240 time to fit residues: 55.4899 Evaluate side-chains 158 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1229 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 136 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 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 613 ASN ** A 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11883 Z= 0.174 Angle : 0.515 12.569 16107 Z= 0.252 Chirality : 0.042 0.141 1839 Planarity : 0.003 0.038 1999 Dihedral : 11.003 166.397 1840 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.99 % Allowed : 23.60 % Favored : 72.41 % 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: -1.90 (0.22), residues: 1409 helix: -0.50 (0.23), residues: 552 sheet: -0.31 (0.35), residues: 215 loop : -2.29 (0.22), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1223 HIS 0.005 0.001 HIS A1198 PHE 0.013 0.001 PHE A 511 TYR 0.013 0.001 TYR C 77 ARG 0.003 0.000 ARG A 786 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 117 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7279 (mp) REVERT: A 349 GLN cc_start: 0.7649 (pt0) cc_final: 0.7287 (pt0) REVERT: A 374 GLN cc_start: 0.7890 (mm-40) cc_final: 0.7510 (mm-40) REVERT: A 626 PHE cc_start: 0.7640 (t80) cc_final: 0.7437 (t80) REVERT: A 679 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8577 (p) REVERT: A 940 MET cc_start: 0.8200 (tmm) cc_final: 0.7912 (ttp) REVERT: A 1193 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6754 (t80) REVERT: C 121 GLN cc_start: 0.7932 (mt0) cc_final: 0.7705 (mt0) REVERT: C 250 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8116 (ttmm) REVERT: C 361 MET cc_start: 0.4820 (ptt) cc_final: 0.4051 (ppp) REVERT: C 366 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7272 (t80) outliers start: 50 outliers final: 34 residues processed: 160 average time/residue: 0.2141 time to fit residues: 51.9142 Evaluate side-chains 151 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 112 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 113 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11883 Z= 0.358 Angle : 0.607 12.288 16107 Z= 0.302 Chirality : 0.046 0.158 1839 Planarity : 0.004 0.041 1999 Dihedral : 10.741 151.118 1835 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.90 % Allowed : 22.09 % Favored : 72.01 % 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: -2.02 (0.22), residues: 1409 helix: -0.70 (0.22), residues: 570 sheet: -0.46 (0.35), residues: 224 loop : -2.27 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 499 HIS 0.010 0.001 HIS A1198 PHE 0.018 0.002 PHE A1205 TYR 0.026 0.002 TYR C 77 ARG 0.006 0.001 ARG A1228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 121 time to evaluate : 1.302 Fit side-chains REVERT: A 188 ASN cc_start: 0.6303 (t0) cc_final: 0.5586 (t0) REVERT: A 349 GLN cc_start: 0.7673 (pt0) cc_final: 0.7317 (pt0) REVERT: A 598 ILE cc_start: 0.4338 (OUTLIER) cc_final: 0.4075 (mt) REVERT: A 679 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8624 (p) REVERT: A 1178 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7320 (mp) REVERT: A 1193 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7289 (t80) REVERT: A 1224 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7774 (tttp) REVERT: C 121 GLN cc_start: 0.7949 (mt0) cc_final: 0.7688 (mt0) REVERT: C 250 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8198 (ttmm) REVERT: C 273 MET cc_start: 0.9024 (mmm) cc_final: 0.8742 (mmt) REVERT: C 361 MET cc_start: 0.4842 (ptt) cc_final: 0.4067 (ppp) REVERT: C 366 TYR cc_start: 0.7969 (OUTLIER) cc_final: 0.7339 (t80) outliers start: 74 outliers final: 54 residues processed: 184 average time/residue: 0.2129 time to fit residues: 58.6262 Evaluate side-chains 172 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 111 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 696 CYS Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1224 LYS Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 45 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 800 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11883 Z= 0.204 Angle : 0.537 12.335 16107 Z= 0.268 Chirality : 0.043 0.140 1839 Planarity : 0.003 0.038 1999 Dihedral : 10.277 141.320 1835 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.63 % Allowed : 23.60 % Favored : 71.77 % 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: -1.73 (0.22), residues: 1409 helix: -0.41 (0.23), residues: 557 sheet: -0.28 (0.35), residues: 218 loop : -2.13 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 499 HIS 0.006 0.001 HIS A1198 PHE 0.014 0.001 PHE A 511 TYR 0.020 0.001 TYR A1192 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 119 time to evaluate : 1.522 Fit side-chains REVERT: A 203 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7307 (mp) REVERT: A 349 GLN cc_start: 0.7650 (pt0) cc_final: 0.7305 (pt0) REVERT: A 374 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7535 (mm-40) REVERT: A 598 ILE cc_start: 0.4323 (OUTLIER) cc_final: 0.4082 (mt) REVERT: A 838 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.7338 (mtt-85) REVERT: A 1178 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7272 (mp) REVERT: A 1193 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7170 (t80) REVERT: A 1224 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7650 (ttmp) REVERT: C 121 GLN cc_start: 0.7938 (mt0) cc_final: 0.7682 (mt0) REVERT: C 192 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8528 (mt) REVERT: C 250 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8200 (ttmm) REVERT: C 273 MET cc_start: 0.9047 (mmm) cc_final: 0.8737 (mmt) REVERT: C 361 MET cc_start: 0.4933 (ptt) cc_final: 0.4278 (ppp) REVERT: C 366 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7415 (t80) outliers start: 58 outliers final: 42 residues processed: 170 average time/residue: 0.2201 time to fit residues: 57.5336 Evaluate side-chains 162 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 112 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1050 ASN Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1224 LYS Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 84 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11883 Z= 0.206 Angle : 0.531 12.331 16107 Z= 0.264 Chirality : 0.043 0.139 1839 Planarity : 0.003 0.039 1999 Dihedral : 9.871 129.311 1833 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.10 % Allowed : 23.13 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1409 helix: -0.28 (0.23), residues: 555 sheet: -0.19 (0.35), residues: 218 loop : -2.08 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 499 HIS 0.006 0.001 HIS A1198 PHE 0.025 0.001 PHE A 419 TYR 0.019 0.001 TYR A1192 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 118 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6352 (t0) cc_final: 0.5680 (t0) REVERT: A 203 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7328 (mp) REVERT: A 349 GLN cc_start: 0.7648 (pt0) cc_final: 0.7308 (pt0) REVERT: A 598 ILE cc_start: 0.4345 (OUTLIER) cc_final: 0.4094 (mt) REVERT: A 800 ASN cc_start: 0.6847 (t0) cc_final: 0.6211 (p0) REVERT: A 940 MET cc_start: 0.8343 (tmm) cc_final: 0.7945 (ttp) REVERT: A 1178 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7304 (mp) REVERT: A 1193 TYR cc_start: 0.8079 (OUTLIER) cc_final: 0.7012 (t80) REVERT: C 121 GLN cc_start: 0.7930 (mt0) cc_final: 0.7687 (mt0) REVERT: C 192 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8543 (mt) REVERT: C 250 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8262 (ttmm) REVERT: C 273 MET cc_start: 0.9063 (mmm) cc_final: 0.8735 (mmt) REVERT: C 361 MET cc_start: 0.4998 (ptt) cc_final: 0.4249 (ppp) REVERT: C 366 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7425 (t80) outliers start: 64 outliers final: 49 residues processed: 172 average time/residue: 0.2056 time to fit residues: 54.0193 Evaluate side-chains 170 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 114 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11883 Z= 0.209 Angle : 0.530 12.354 16107 Z= 0.265 Chirality : 0.043 0.140 1839 Planarity : 0.003 0.038 1999 Dihedral : 9.651 114.364 1831 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.02 % Allowed : 23.29 % Favored : 71.69 % 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: -1.52 (0.22), residues: 1409 helix: -0.24 (0.23), residues: 556 sheet: -0.13 (0.35), residues: 218 loop : -2.03 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 499 HIS 0.006 0.001 HIS A1198 PHE 0.018 0.001 PHE A 419 TYR 0.020 0.001 TYR A1192 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 116 time to evaluate : 1.365 Fit side-chains revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7324 (mp) REVERT: A 349 GLN cc_start: 0.7641 (pt0) cc_final: 0.7310 (pt0) REVERT: A 374 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7506 (mm-40) REVERT: A 598 ILE cc_start: 0.4436 (OUTLIER) cc_final: 0.4178 (mt) REVERT: A 800 ASN cc_start: 0.6786 (t0) cc_final: 0.6076 (p0) REVERT: A 1178 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7304 (mp) REVERT: A 1193 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.7013 (t80) REVERT: C 121 GLN cc_start: 0.7877 (mt0) cc_final: 0.7645 (mt0) REVERT: C 250 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8252 (ttmm) REVERT: C 273 MET cc_start: 0.9065 (mmm) cc_final: 0.8741 (mmt) REVERT: C 361 MET cc_start: 0.5040 (ptt) cc_final: 0.4296 (ppp) REVERT: C 366 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7274 (t80) outliers start: 63 outliers final: 51 residues processed: 171 average time/residue: 0.2018 time to fit residues: 53.0507 Evaluate side-chains 171 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 114 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 299 TRP Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1043 SER Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 258 GLU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 0.2980 chunk 130 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 114 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11883 Z= 0.132 Angle : 0.496 12.431 16107 Z= 0.247 Chirality : 0.041 0.138 1839 Planarity : 0.003 0.038 1999 Dihedral : 9.308 104.209 1831 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.99 % Allowed : 24.56 % Favored : 71.45 % 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: -1.30 (0.23), residues: 1409 helix: -0.01 (0.24), residues: 550 sheet: -0.05 (0.35), residues: 221 loop : -1.94 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1223 HIS 0.003 0.001 HIS A1198 PHE 0.016 0.001 PHE A 419 TYR 0.018 0.001 TYR A1192 ARG 0.003 0.000 ARG A 838 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 124 time to evaluate : 1.293 Fit side-chains revert: symmetry clash REVERT: A 188 ASN cc_start: 0.6360 (t0) cc_final: 0.5700 (t0) REVERT: A 203 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7310 (mp) REVERT: A 349 GLN cc_start: 0.7618 (pt0) cc_final: 0.7290 (pt0) REVERT: A 374 GLN cc_start: 0.8005 (mm-40) cc_final: 0.7444 (mm-40) REVERT: A 419 PHE cc_start: 0.8718 (m-10) cc_final: 0.8496 (m-10) REVERT: A 598 ILE cc_start: 0.4424 (OUTLIER) cc_final: 0.4174 (mt) REVERT: A 800 ASN cc_start: 0.6768 (t0) cc_final: 0.6038 (p0) REVERT: A 1178 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7312 (mp) REVERT: C 71 GLN cc_start: 0.8150 (mp10) cc_final: 0.7892 (mt0) REVERT: C 250 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8258 (ttmm) REVERT: C 273 MET cc_start: 0.9114 (mmm) cc_final: 0.8778 (mmt) REVERT: C 361 MET cc_start: 0.4920 (ptt) cc_final: 0.4202 (ppp) REVERT: C 366 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7228 (t80) outliers start: 50 outliers final: 38 residues processed: 167 average time/residue: 0.2088 time to fit residues: 52.4610 Evaluate side-chains 163 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11883 Z= 0.284 Angle : 0.564 12.211 16107 Z= 0.282 Chirality : 0.044 0.153 1839 Planarity : 0.003 0.039 1999 Dihedral : 9.485 103.080 1831 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.91 % Allowed : 24.48 % Favored : 71.61 % 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: -1.48 (0.22), residues: 1409 helix: -0.28 (0.23), residues: 567 sheet: -0.11 (0.35), residues: 227 loop : -1.98 (0.24), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 499 HIS 0.007 0.001 HIS A1198 PHE 0.016 0.002 PHE A 419 TYR 0.026 0.002 TYR C 77 ARG 0.003 0.000 ARG A 838 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2818 Ramachandran restraints generated. 1409 Oldfield, 0 Emsley, 1409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 1.269 Fit side-chains REVERT: A 203 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7336 (mp) REVERT: A 349 GLN cc_start: 0.7654 (pt0) cc_final: 0.7318 (pt0) REVERT: A 374 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7474 (mm-40) REVERT: A 419 PHE cc_start: 0.8738 (m-10) cc_final: 0.8536 (m-10) REVERT: A 598 ILE cc_start: 0.4578 (OUTLIER) cc_final: 0.4321 (mt) REVERT: A 800 ASN cc_start: 0.6771 (t0) cc_final: 0.6103 (p0) REVERT: A 838 ARG cc_start: 0.7577 (mtt-85) cc_final: 0.7316 (mtp180) REVERT: A 940 MET cc_start: 0.8391 (tmm) cc_final: 0.7975 (ttp) REVERT: A 1178 ILE cc_start: 0.7902 (OUTLIER) cc_final: 0.7303 (mp) REVERT: A 1193 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7086 (t80) REVERT: A 1224 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7669 (ttmp) REVERT: C 121 GLN cc_start: 0.8188 (mt0) cc_final: 0.7942 (mt0) REVERT: C 250 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8231 (ttmm) REVERT: C 361 MET cc_start: 0.5057 (ptt) cc_final: 0.4312 (ppp) REVERT: C 366 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7207 (t80) outliers start: 49 outliers final: 39 residues processed: 160 average time/residue: 0.2020 time to fit residues: 48.9836 Evaluate side-chains 161 residues out of total 1254 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 115 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 463 SER Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 635 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 679 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 706 SER Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 844 ASN Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 962 ILE Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1153 VAL Chi-restraints excluded: chain A residue 1154 THR Chi-restraints excluded: chain A residue 1178 ILE Chi-restraints excluded: chain A residue 1193 TYR Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1224 LYS Chi-restraints excluded: chain A residue 1234 THR Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 250 LYS Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 chunk 6 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.104484 restraints weight = 15525.397| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.27 r_work: 0.3019 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11883 Z= 0.160 Angle : 0.512 12.231 16107 Z= 0.256 Chirality : 0.042 0.151 1839 Planarity : 0.003 0.038 1999 Dihedral : 9.260 101.426 1831 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.59 % Allowed : 24.96 % Favored : 71.45 % 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 (0.23), residues: 1409 helix: -0.03 (0.23), residues: 554 sheet: 0.02 (0.36), residues: 221 loop : -1.93 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1223 HIS 0.004 0.001 HIS A1198 PHE 0.016 0.001 PHE A 419 TYR 0.023 0.001 TYR C 77 ARG 0.003 0.000 ARG A 838 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2686.68 seconds wall clock time: 49 minutes 37.17 seconds (2977.17 seconds total)