Starting phenix.real_space_refine on Sat Feb 17 20:31:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tny_10539/02_2024/6tny_10539_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tny_10539/02_2024/6tny_10539.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tny_10539/02_2024/6tny_10539_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tny_10539/02_2024/6tny_10539_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tny_10539/02_2024/6tny_10539_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tny_10539/02_2024/6tny_10539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tny_10539/02_2024/6tny_10539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tny_10539/02_2024/6tny_10539_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tny_10539/02_2024/6tny_10539_neut_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 1 6.06 5 P 53 5.49 5 S 125 5.16 5 C 12326 2.51 5 N 3377 2.21 5 O 3840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A ARG 311": "NH1" <-> "NH2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 470": "NH1" <-> "NH2" Residue "A GLU 534": "OE1" <-> "OE2" Residue "A ARG 549": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A TYR 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A GLU 830": "OE1" <-> "OE2" Residue "A ARG 855": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 921": "NH1" <-> "NH2" Residue "A GLU 976": "OE1" <-> "OE2" Residue "A GLU 980": "OE1" <-> "OE2" Residue "A ARG 1082": "NH1" <-> "NH2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A ARG 1098": "NH1" <-> "NH2" Residue "B PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B GLU 274": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 366": "OE1" <-> "OE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 86": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E GLU 192": "OE1" <-> "OE2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F GLU 193": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G GLU 201": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19726 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7926 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1010, 7922 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 1010, 7922 Classifications: {'peptide': 1010} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 942} Chain breaks: 3 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 8085 Chain: "B" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3304 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 399} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1130 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "D" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 554 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 7, 'TRANS': 58} Chain: "E" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1924 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1913 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1913 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 7, 'TRANS': 241} Chain breaks: 1 Chain: "P" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 469 Unusual residues: {'DOC': 1} Classifications: {'DNA': 22, 'undetermined': 1} Link IDs: {'rna3p': 21, None: 1} Not linked: pdbres=" DG P 24 " pdbres="DOC P 25 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "T" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 555 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' ZN': 1, 'SF4': 1, 'TTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7157 SG CYS A1012 93.068 71.259 44.294 1.00 40.62 S ATOM 7175 SG CYS A1015 95.509 70.329 47.207 1.00 40.62 S ATOM 7248 SG CYS A1026 96.869 69.692 43.613 1.00 40.62 S ATOM 7264 SG CYS A1029 93.666 68.034 44.806 1.00 40.62 S ATOM 7616 SG CYS A1071 58.117 95.238 52.833 1.00 40.62 S ATOM 7654 SG CYS A1076 59.246 90.776 56.637 1.00 30.94 S ATOM 7515 SG CYS A1058 59.456 89.840 49.733 1.00 40.62 S ATOM 7541 SG CYS A1061 54.296 90.957 53.405 1.00 24.79 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLY A1100 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A1100 " occ=0.50 Time building chain proxies: 15.87, per 1000 atoms: 0.80 Number of scatterers: 19726 At special positions: 0 Unit cell: (145.29, 161.82, 137.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 4 26.01 S 125 16.00 P 53 15.00 O 3840 8.00 N 3377 7.00 C 12326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.49 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1202 " pdb="FE2 SF4 A1202 " - pdb=" SG CYS A1076 " pdb="FE1 SF4 A1202 " - pdb=" SG CYS A1071 " pdb="FE3 SF4 A1202 " - pdb=" SG CYS A1058 " pdb="FE4 SF4 A1202 " - pdb=" SG CYS A1061 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1201 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1029 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1015 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1012 " pdb="ZN ZN A1201 " - pdb=" SG CYS A1026 " Number of angles added : 6 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4502 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 23 sheets defined 26.8% alpha, 21.2% beta 22 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 9.17 Creating SS restraints... Processing helix chain 'A' and resid 161 through 168 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 217 through 227 removed outlier: 3.720A pdb=" N VAL A 220 " --> pdb=" O PRO A 217 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ALA A 221 " --> pdb=" O ARG A 218 " (cutoff:3.500A) Proline residue: A 222 - end of helix removed outlier: 4.150A pdb=" N LEU A 227 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 Processing helix chain 'A' and resid 302 through 305 removed outlier: 3.591A pdb=" N GLN A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 305' Processing helix chain 'A' and resid 374 through 388 Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 459 through 466 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 502 through 525 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 528 through 539 Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 606 through 613 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 656 through 676 removed outlier: 4.732A pdb=" N LYS A 676 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 704 removed outlier: 3.886A pdb=" N TYR A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 738 Processing helix chain 'A' and resid 768 through 782 Processing helix chain 'A' and resid 838 through 852 Processing helix chain 'A' and resid 857 through 872 Processing helix chain 'A' and resid 899 through 905 Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 963 through 971 removed outlier: 3.931A pdb=" N GLU A 971 " --> pdb=" O LEU A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 989 Processing helix chain 'A' and resid 1002 through 1004 No H-bonds generated for 'chain 'A' and resid 1002 through 1004' Processing helix chain 'A' and resid 1034 through 1055 removed outlier: 4.884A pdb=" N GLU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL A1041 " --> pdb=" O TYR A1037 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS A1043 " --> pdb=" O LYS A1039 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A1052 " --> pdb=" O GLU A1048 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A1053 " --> pdb=" O GLU A1049 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A1054 " --> pdb=" O ARG A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1062 Processing helix chain 'A' and resid 1078 through 1081 No H-bonds generated for 'chain 'A' and resid 1078 through 1081' Processing helix chain 'A' and resid 1084 through 1095 removed outlier: 3.567A pdb=" N GLN A1094 " --> pdb=" O GLU A1090 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 7 No H-bonds generated for 'chain 'B' and resid 5 through 7' Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 51 through 73 removed outlier: 3.694A pdb=" N ALA B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 56 " --> pdb=" O HIS B 52 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.900A pdb=" N GLN B 71 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 223 Processing helix chain 'B' and resid 229 through 235 Processing helix chain 'B' and resid 273 through 287 removed outlier: 3.971A pdb=" N LYS B 277 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 348 through 354 Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 23 through 29 Processing helix chain 'C' and resid 34 through 51 Processing helix chain 'C' and resid 85 through 91 Processing helix chain 'C' and resid 113 through 123 removed outlier: 4.146A pdb=" N ASP C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 52 removed outlier: 3.669A pdb=" N LEU D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'E' and resid 10 through 17 Processing helix chain 'E' and resid 72 through 81 removed outlier: 4.224A pdb=" N CYS E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 152 Processing helix chain 'E' and resid 209 through 221 removed outlier: 3.557A pdb=" N LYS E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ALA E 218 " --> pdb=" O PHE E 214 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR E 219 " --> pdb=" O PHE E 215 " (cutoff:3.500A) Proline residue: E 220 - end of helix Processing helix chain 'F' and resid 9 through 19 removed outlier: 3.874A pdb=" N LEU F 19 " --> pdb=" O VAL F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 78 Processing helix chain 'F' and resid 141 through 153 removed outlier: 4.193A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 removed outlier: 4.430A pdb=" N LYS F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 221 No H-bonds generated for 'chain 'F' and resid 219 through 221' Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.617A pdb=" N LEU G 19 " --> pdb=" O VAL G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 78 Processing helix chain 'G' and resid 141 through 154 removed outlier: 3.591A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 221 removed outlier: 4.616A pdb=" N LYS G 217 " --> pdb=" O ASN G 213 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA G 218 " --> pdb=" O PHE G 214 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N THR G 219 " --> pdb=" O PHE G 215 " (cutoff:3.500A) Proline residue: G 220 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 295 through 298 removed outlier: 4.300A pdb=" N TRP A 265 " --> pdb=" O HIS A 298 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N PHE A 128 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE A 101 " --> pdb=" O ARG A 126 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG A 126 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N HIS A 103 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N VAL A 124 " --> pdb=" O HIS A 103 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU A 286 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N HIS A 140 " --> pdb=" O LEU A 286 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA A 288 " --> pdb=" O HIS A 140 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N HIS A 142 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N VAL A 290 " --> pdb=" O HIS A 142 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 147 through 151 Processing sheet with id= C, first strand: chain 'A' and resid 455 through 458 removed outlier: 3.914A pdb=" N GLY A 395 " --> pdb=" O MET A 457 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE A 315 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 336 " --> pdb=" O GLU A 318 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS A 367 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR A 356 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLN A 369 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 431 through 438 Processing sheet with id= E, first strand: chain 'A' and resid 592 through 594 removed outlier: 6.981A pdb=" N ARG A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 792 through 798 removed outlier: 6.932A pdb=" N THR A 600 " --> pdb=" O GLU A 795 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL A 797 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE A 598 " --> pdb=" O VAL A 797 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 753 " --> pdb=" O MET A 760 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 762 " --> pdb=" O VAL A 751 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N VAL A 751 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 637 through 639 Processing sheet with id= H, first strand: chain 'A' and resid 883 through 886 Processing sheet with id= I, first strand: chain 'B' and resid 141 through 143 removed outlier: 3.652A pdb=" N GLU B 132 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP B 175 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N SER B 164 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL B 173 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 447 through 451 removed outlier: 7.725A pdb=" N LEU B 197 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL B 241 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL B 199 " --> pdb=" O VAL B 241 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU B 243 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B 243 " --> pdb=" O PRO B 291 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 293 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 332 through 336 removed outlier: 6.607A pdb=" N VAL B 401 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N TYR B 402 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 424 " --> pdb=" O TYR B 402 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY B 411 " --> pdb=" O THR B 427 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 73 through 80 removed outlier: 5.731A pdb=" N LEU C 62 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL C 100 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N SER C 64 " --> pdb=" O ILE C 98 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ILE C 98 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 2 through 6 Processing sheet with id= N, first strand: chain 'E' and resid 66 through 71 removed outlier: 7.298A pdb=" N GLU E 25 " --> pdb=" O MET E 40 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET E 40 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N CYS E 27 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLN E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS E 240 " --> pdb=" O THR E 224 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR E 224 " --> pdb=" O LYS E 240 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 203 through 208 removed outlier: 6.013A pdb=" N ALA E 157 " --> pdb=" O SER E 172 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N SER E 172 " --> pdb=" O ALA E 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 59 through 62 Processing sheet with id= Q, first strand: chain 'F' and resid 25 through 28 Processing sheet with id= R, first strand: chain 'F' and resid 34 through 40 removed outlier: 5.607A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 203 through 208 Processing sheet with id= T, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.646A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 25 through 30 Processing sheet with id= V, first strand: chain 'G' and resid 34 through 40 removed outlier: 5.330A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 203 through 208 removed outlier: 5.985A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) 713 hydrogen bonds defined for protein. 2001 hydrogen bond angles defined for protein. Warning, Cannot make NA restraints for OD residue Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 10.77 Time building geometry restraints manager: 10.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 8016 1.40 - 1.63: 11994 1.63 - 1.85: 188 1.85 - 2.08: 0 2.08 - 2.31: 12 Bond restraints: 20210 Sorted by residual: bond pdb=" C4' DOC P 25 " pdb=" O4' DOC P 25 " ideal model delta sigma weight residual 1.609 1.278 0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" C2' TTP A1203 " pdb=" C3' TTP A1203 " ideal model delta sigma weight residual 1.524 1.216 0.308 2.00e-02 2.50e+03 2.36e+02 bond pdb=" O4' DOC P 25 " pdb=" C1' DOC P 25 " ideal model delta sigma weight residual 1.268 1.552 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C4' DOC P 25 " pdb=" C3' DOC P 25 " ideal model delta sigma weight residual 1.334 1.615 -0.281 2.00e-02 2.50e+03 1.98e+02 bond pdb=" C3' DOC P 25 " pdb=" C2' DOC P 25 " ideal model delta sigma weight residual 1.489 1.305 0.184 2.00e-02 2.50e+03 8.47e+01 ... (remaining 20205 not shown) Histogram of bond angle deviations from ideal: 72.64 - 84.96: 12 84.96 - 97.28: 0 97.28 - 109.60: 3418 109.60 - 121.92: 19692 121.92 - 134.24: 4487 Bond angle restraints: 27609 Sorted by residual: angle pdb=" N ARG A 985 " pdb=" CA ARG A 985 " pdb=" C ARG A 985 " ideal model delta sigma weight residual 111.07 102.80 8.27 1.07e+00 8.73e-01 5.98e+01 angle pdb=" N ALA B 179 " pdb=" CA ALA B 179 " pdb=" C ALA B 179 " ideal model delta sigma weight residual 111.28 119.44 -8.16 1.09e+00 8.42e-01 5.60e+01 angle pdb=" N ARG A1098 " pdb=" CA ARG A1098 " pdb=" C ARG A1098 " ideal model delta sigma weight residual 111.36 103.72 7.64 1.09e+00 8.42e-01 4.92e+01 angle pdb=" N GLY A 592 " pdb=" CA GLY A 592 " pdb=" C GLY A 592 " ideal model delta sigma weight residual 110.20 118.98 -8.78 1.32e+00 5.74e-01 4.42e+01 angle pdb=" N ALA A1024 " pdb=" CA ALA A1024 " pdb=" C ALA A1024 " ideal model delta sigma weight residual 111.28 118.45 -7.17 1.09e+00 8.42e-01 4.32e+01 ... (remaining 27604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.54: 11320 27.54 - 55.09: 770 55.09 - 82.63: 68 82.63 - 110.18: 14 110.18 - 137.72: 2 Dihedral angle restraints: 12174 sinusoidal: 5211 harmonic: 6963 Sorted by residual: dihedral pdb=" C2 TTP A1203 " pdb=" C1' TTP A1203 " pdb=" N1 TTP A1203 " pdb=" O4' TTP A1203 " ideal model delta sinusoidal sigma weight residual 301.68 163.96 137.72 1 2.00e+01 2.50e-03 4.18e+01 dihedral pdb=" N HIS A1021 " pdb=" C HIS A1021 " pdb=" CA HIS A1021 " pdb=" CB HIS A1021 " ideal model delta harmonic sigma weight residual 122.80 137.51 -14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" C5' TTP A1203 " pdb=" O5' TTP A1203 " pdb=" PA TTP A1203 " pdb=" O3A TTP A1203 " ideal model delta sinusoidal sigma weight residual 179.97 65.20 114.77 1 2.00e+01 2.50e-03 3.41e+01 ... (remaining 12171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2815 0.099 - 0.197: 313 0.197 - 0.296: 21 0.296 - 0.394: 0 0.394 - 0.493: 3 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CA ASP B 180 " pdb=" N ASP B 180 " pdb=" C ASP B 180 " pdb=" CB ASP B 180 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.07e+00 chirality pdb=" CA HIS A1021 " pdb=" N HIS A1021 " pdb=" C HIS A1021 " pdb=" CB HIS A1021 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CB ILE A1078 " pdb=" CA ILE A1078 " pdb=" CG1 ILE A1078 " pdb=" CG2 ILE A1078 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 3149 not shown) Planarity restraints: 3387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C PHE A1099 " 0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" N AGLY A1100 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1099 " -0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C PHE A1099 " 0.079 2.00e-02 2.50e+03 pdb=" O PHE A1099 " -0.029 2.00e-02 2.50e+03 pdb=" N BGLY A1100 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS B 128 " -0.050 5.00e-02 4.00e+02 7.49e-02 8.98e+00 pdb=" N PRO B 129 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " -0.041 5.00e-02 4.00e+02 ... (remaining 3384 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 59 2.44 - 3.06: 10630 3.06 - 3.67: 28337 3.67 - 4.29: 41469 4.29 - 4.90: 68900 Nonbonded interactions: 149395 Sorted by model distance: nonbonded pdb=" OE1 GLN B 308 " pdb=" ND2 ASN B 330 " model vdw 1.826 2.520 nonbonded pdb=" CG1 VAL A 861 " pdb=" NE ARG A 985 " model vdw 1.943 3.540 nonbonded pdb=" O GLN B 308 " pdb=" CG2 THR B 329 " model vdw 2.129 3.460 nonbonded pdb=" O CYS A1011 " pdb=" NH2 ARG A1098 " model vdw 2.224 2.520 nonbonded pdb=" CG1 VAL A 861 " pdb=" CD ARG A 985 " model vdw 2.251 3.860 ... (remaining 149390 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 'E' and (resid 1 through 107 or resid 109 through 185 or resid 191 or res \ id 194 through 255)) selection = (chain 'F' and (resid 1 through 191 or resid 194 through 255)) selection = (chain 'G' and (resid 1 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 109 through 185 or resid 193 through 255)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.320 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: 0.000 Extract box with map and model: 22.690 Check model and map are aligned: 0.300 Set scattering table: 0.210 Process input model: 80.060 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.331 20210 Z= 0.591 Angle : 1.100 11.449 27609 Z= 0.618 Chirality : 0.063 0.493 3152 Planarity : 0.009 0.075 3387 Dihedral : 17.680 137.722 7672 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.42 % Favored : 93.24 % Rotamer: Outliers : 0.83 % Allowed : 8.84 % Favored : 90.33 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -3.49 (0.15), residues: 2370 helix: -2.41 (0.16), residues: 669 sheet: -0.89 (0.20), residues: 604 loop : -3.10 (0.15), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP A 344 HIS 0.011 0.002 HIS C 99 PHE 0.032 0.003 PHE A 637 TYR 0.025 0.003 TYR A 618 ARG 0.013 0.001 ARG A 276 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 282 time to evaluate : 2.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 GLU cc_start: 0.4441 (OUTLIER) cc_final: 0.3914 (tp30) REVERT: E 118 LEU cc_start: 0.4217 (mm) cc_final: 0.4000 (tp) REVERT: E 130 GLU cc_start: 0.5212 (mm-30) cc_final: 0.4975 (tp30) REVERT: G 116 MET cc_start: 0.5901 (ttp) cc_final: 0.5585 (tpt) outliers start: 17 outliers final: 6 residues processed: 297 average time/residue: 0.4081 time to fit residues: 170.0788 Evaluate side-chains 179 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 172 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 48 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 4.9990 chunk 182 optimal weight: 0.0030 chunk 101 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 558 GLN A 726 GLN A 842 ASN A 865 GLN A 948 HIS ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 HIS A1092 GLN B 21 ASN B 49 GLN B 70 GLN B 86 GLN B 140 GLN B 184 GLN C 58 HIS E 65 ASN E 125 GLN F 65 ASN F 200 ASN F 204 GLN G 49 GLN ** G 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20210 Z= 0.189 Angle : 0.637 8.944 27609 Z= 0.335 Chirality : 0.044 0.188 3152 Planarity : 0.006 0.059 3387 Dihedral : 15.324 142.692 3172 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 1.94 % Allowed : 13.41 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -2.24 (0.16), residues: 2370 helix: -0.74 (0.20), residues: 674 sheet: -0.37 (0.20), residues: 635 loop : -2.74 (0.16), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 28 HIS 0.018 0.001 HIS A1021 PHE 0.018 0.001 PHE E 144 TYR 0.017 0.001 TYR G 211 ARG 0.010 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 202 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1087 LYS cc_start: 0.7777 (mmtm) cc_final: 0.7504 (mmtt) REVERT: E 28 TRP cc_start: 0.7851 (m-10) cc_final: 0.7540 (m-10) REVERT: E 118 LEU cc_start: 0.4021 (mm) cc_final: 0.3247 (tp) REVERT: E 119 MET cc_start: 0.4346 (pmm) cc_final: 0.2242 (ptt) REVERT: E 199 MET cc_start: 0.4006 (OUTLIER) cc_final: 0.3563 (mmm) REVERT: E 201 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7165 (tm-30) REVERT: G 116 MET cc_start: 0.5917 (ttp) cc_final: 0.5684 (tpt) REVERT: G 199 MET cc_start: 0.6934 (ppp) cc_final: 0.6141 (ppp) outliers start: 40 outliers final: 20 residues processed: 229 average time/residue: 0.3683 time to fit residues: 124.6681 Evaluate side-chains 182 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 161 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 21 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 182 optimal weight: 20.0000 chunk 149 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 175 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 GLN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 127 GLN D 68 GLN D 91 HIS D 103 HIS E 8 GLN G 49 GLN ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 108 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 20210 Z= 0.451 Angle : 0.803 9.673 27609 Z= 0.414 Chirality : 0.050 0.215 3152 Planarity : 0.007 0.058 3387 Dihedral : 15.509 138.113 3163 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.90 % Favored : 92.02 % Rotamer: Outliers : 3.35 % Allowed : 15.55 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -2.16 (0.16), residues: 2370 helix: -0.62 (0.19), residues: 680 sheet: -0.36 (0.21), residues: 624 loop : -2.68 (0.17), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP A 79 HIS 0.038 0.003 HIS A 160 PHE 0.025 0.003 PHE A 350 TYR 0.032 0.002 TYR A1080 ARG 0.013 0.001 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 166 time to evaluate : 2.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 GLN cc_start: 0.8190 (mp10) cc_final: 0.7873 (mm-40) REVERT: A 1087 LYS cc_start: 0.7996 (mmtm) cc_final: 0.7718 (mmtt) REVERT: B 299 PHE cc_start: 0.5876 (OUTLIER) cc_final: 0.5410 (m-80) REVERT: C 7 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8739 (tt) REVERT: E 28 TRP cc_start: 0.7859 (m-10) cc_final: 0.7624 (m-10) REVERT: E 118 LEU cc_start: 0.4176 (OUTLIER) cc_final: 0.3176 (mm) REVERT: E 119 MET cc_start: 0.4289 (pmm) cc_final: 0.2752 (ptt) REVERT: E 215 PHE cc_start: 0.5690 (m-10) cc_final: 0.4660 (m-10) REVERT: G 119 MET cc_start: 0.6669 (mpp) cc_final: 0.6324 (mpp) REVERT: G 199 MET cc_start: 0.7269 (ppp) cc_final: 0.6511 (ppp) outliers start: 69 outliers final: 41 residues processed: 220 average time/residue: 0.3603 time to fit residues: 120.2586 Evaluate side-chains 202 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 158 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1074 ARG Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 358 MET Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 239 TYR Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 20.0000 chunk 164 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 104 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 220 optimal weight: 0.9980 chunk 232 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 52 HIS ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 68 GLN ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 71 ASN G 107 ASN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20210 Z= 0.173 Angle : 0.608 10.221 27609 Z= 0.316 Chirality : 0.043 0.177 3152 Planarity : 0.005 0.052 3387 Dihedral : 15.216 142.223 3162 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.77 % Favored : 95.18 % Rotamer: Outliers : 2.53 % Allowed : 17.06 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.50 (0.17), residues: 2370 helix: 0.20 (0.21), residues: 672 sheet: -0.07 (0.21), residues: 628 loop : -2.42 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 381 HIS 0.013 0.001 HIS A1021 PHE 0.021 0.001 PHE E 215 TYR 0.015 0.001 TYR E 249 ARG 0.008 0.000 ARG F 146 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 179 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 299 PHE cc_start: 0.5795 (OUTLIER) cc_final: 0.5425 (m-80) REVERT: E 118 LEU cc_start: 0.3954 (OUTLIER) cc_final: 0.3038 (mm) REVERT: E 119 MET cc_start: 0.4469 (pmm) cc_final: 0.2790 (ptt) REVERT: E 205 LEU cc_start: 0.4061 (OUTLIER) cc_final: 0.3621 (mp) REVERT: E 211 TYR cc_start: 0.7623 (m-80) cc_final: 0.7367 (m-80) REVERT: E 215 PHE cc_start: 0.5912 (m-10) cc_final: 0.5216 (m-10) REVERT: F 149 ARG cc_start: 0.7296 (ptm160) cc_final: 0.7089 (ttp-110) REVERT: G 119 MET cc_start: 0.6738 (mpp) cc_final: 0.6532 (mpp) REVERT: G 199 MET cc_start: 0.7205 (ppp) cc_final: 0.6463 (ppp) REVERT: G 229 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6373 (ppp) outliers start: 52 outliers final: 32 residues processed: 214 average time/residue: 0.3561 time to fit residues: 113.9059 Evaluate side-chains 191 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 861 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 229 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 3 optimal weight: 0.0970 chunk 173 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 198 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 209 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN A 636 GLN A 948 HIS A 955 GLN ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20210 Z= 0.265 Angle : 0.662 14.415 27609 Z= 0.338 Chirality : 0.045 0.171 3152 Planarity : 0.005 0.051 3387 Dihedral : 15.040 139.784 3162 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.21 % Favored : 93.71 % Rotamer: Outliers : 2.96 % Allowed : 17.83 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.37 (0.17), residues: 2370 helix: 0.34 (0.21), residues: 675 sheet: -0.03 (0.21), residues: 617 loop : -2.33 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 28 HIS 0.011 0.001 HIS A1021 PHE 0.021 0.002 PHE E 215 TYR 0.020 0.002 TYR A1080 ARG 0.007 0.001 ARG A 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 166 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5493 (tpp) cc_final: 0.5243 (tpp) REVERT: A 165 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7530 (mm-40) REVERT: B 299 PHE cc_start: 0.5722 (OUTLIER) cc_final: 0.5416 (m-80) REVERT: C 43 ASP cc_start: 0.6666 (t70) cc_final: 0.6417 (t0) REVERT: E 118 LEU cc_start: 0.4087 (mm) cc_final: 0.3152 (mm) REVERT: E 119 MET cc_start: 0.4425 (pmm) cc_final: 0.3089 (ptt) REVERT: F 149 ARG cc_start: 0.7389 (ptm160) cc_final: 0.7127 (ttp-110) REVERT: G 91 ARG cc_start: 0.5276 (OUTLIER) cc_final: 0.4887 (mtm-85) REVERT: G 199 MET cc_start: 0.7264 (ppp) cc_final: 0.6515 (ppp) outliers start: 61 outliers final: 39 residues processed: 214 average time/residue: 0.3274 time to fit residues: 107.6324 Evaluate side-chains 197 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 91 ARG Chi-restraints excluded: chain G residue 160 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 0.0170 chunk 209 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 184 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN E 38 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20210 Z= 0.235 Angle : 0.635 12.994 27609 Z= 0.325 Chirality : 0.044 0.172 3152 Planarity : 0.005 0.050 3387 Dihedral : 14.931 140.214 3162 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.58 % Favored : 94.38 % Rotamer: Outliers : 3.06 % Allowed : 18.56 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.18 (0.17), residues: 2370 helix: 0.53 (0.21), residues: 672 sheet: 0.24 (0.21), residues: 586 loop : -2.26 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 28 HIS 0.012 0.001 HIS A1021 PHE 0.015 0.001 PHE E 215 TYR 0.017 0.001 TYR A1080 ARG 0.010 0.001 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 168 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5688 (tpp) cc_final: 0.5392 (tpp) REVERT: A 165 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7351 (mm-40) REVERT: B 299 PHE cc_start: 0.5718 (OUTLIER) cc_final: 0.5508 (m-80) REVERT: C 7 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 43 ASP cc_start: 0.6695 (t70) cc_final: 0.6455 (t0) REVERT: E 28 TRP cc_start: 0.7868 (m100) cc_final: 0.7587 (m100) REVERT: E 118 LEU cc_start: 0.4046 (mm) cc_final: 0.3038 (mm) REVERT: E 119 MET cc_start: 0.4681 (pmm) cc_final: 0.3224 (ptt) REVERT: E 215 PHE cc_start: 0.6424 (m-10) cc_final: 0.5860 (m-10) REVERT: G 79 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6415 (mm) REVERT: G 199 MET cc_start: 0.7174 (ppp) cc_final: 0.6469 (ppp) outliers start: 63 outliers final: 51 residues processed: 214 average time/residue: 0.3421 time to fit residues: 113.2742 Evaluate side-chains 211 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 157 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain B residue 20 ASN Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 131 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 232 optimal weight: 10.0000 chunk 145 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 125 ASN E 38 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20210 Z= 0.197 Angle : 0.615 12.450 27609 Z= 0.315 Chirality : 0.043 0.207 3152 Planarity : 0.005 0.048 3387 Dihedral : 14.837 140.940 3162 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.62 % Allowed : 19.24 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2370 helix: 0.79 (0.21), residues: 660 sheet: 0.30 (0.22), residues: 587 loop : -2.14 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 28 HIS 0.010 0.001 HIS A1021 PHE 0.016 0.001 PHE E 215 TYR 0.018 0.001 TYR E 249 ARG 0.009 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 169 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5667 (tpp) cc_final: 0.5336 (tpp) REVERT: A 165 GLN cc_start: 0.7879 (mm-40) cc_final: 0.7334 (mm-40) REVERT: B 295 MET cc_start: 0.7295 (mmm) cc_final: 0.6648 (mtt) REVERT: C 7 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8635 (tt) REVERT: E 28 TRP cc_start: 0.7873 (m100) cc_final: 0.7603 (m100) REVERT: E 118 LEU cc_start: 0.4079 (mm) cc_final: 0.3032 (mm) REVERT: E 119 MET cc_start: 0.4935 (pmm) cc_final: 0.3376 (ptt) REVERT: E 130 GLU cc_start: 0.5499 (tp30) cc_final: 0.5230 (tp30) REVERT: F 149 ARG cc_start: 0.7490 (ptm160) cc_final: 0.7275 (ttp-110) REVERT: G 79 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6293 (mm) outliers start: 54 outliers final: 44 residues processed: 210 average time/residue: 0.3250 time to fit residues: 104.4070 Evaluate side-chains 201 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 155 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 138 optimal weight: 0.0060 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 182 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20210 Z= 0.262 Angle : 0.655 11.865 27609 Z= 0.334 Chirality : 0.044 0.167 3152 Planarity : 0.005 0.048 3387 Dihedral : 14.853 140.365 3160 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.17 % Favored : 93.79 % Rotamer: Outliers : 2.82 % Allowed : 19.68 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.03 (0.17), residues: 2370 helix: 0.71 (0.21), residues: 661 sheet: 0.28 (0.21), residues: 590 loop : -2.17 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 28 HIS 0.009 0.001 HIS A1021 PHE 0.019 0.002 PHE G 144 TYR 0.018 0.002 TYR A1080 ARG 0.011 0.001 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 161 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5792 (tpp) cc_final: 0.5448 (tpp) REVERT: A 165 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7351 (mm-40) REVERT: B 295 MET cc_start: 0.7431 (mmm) cc_final: 0.6576 (mtt) REVERT: C 7 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8651 (tt) REVERT: E 28 TRP cc_start: 0.7848 (m100) cc_final: 0.7558 (m100) REVERT: E 118 LEU cc_start: 0.4472 (OUTLIER) cc_final: 0.3836 (mm) REVERT: F 149 ARG cc_start: 0.7512 (ptm160) cc_final: 0.7077 (ttp-110) outliers start: 58 outliers final: 51 residues processed: 204 average time/residue: 0.3390 time to fit residues: 105.3072 Evaluate side-chains 210 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 157 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 0.0770 chunk 203 optimal weight: 7.9990 chunk 216 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 195 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 20210 Z= 0.399 Angle : 0.752 10.882 27609 Z= 0.383 Chirality : 0.048 0.185 3152 Planarity : 0.006 0.060 3387 Dihedral : 15.049 138.725 3160 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.27 % Favored : 92.61 % Rotamer: Outliers : 2.92 % Allowed : 19.92 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % 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: -1.38 (0.17), residues: 2370 helix: 0.27 (0.20), residues: 661 sheet: 0.16 (0.22), residues: 574 loop : -2.29 (0.17), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 28 HIS 0.010 0.002 HIS C 99 PHE 0.019 0.002 PHE A1099 TYR 0.028 0.002 TYR A1080 ARG 0.011 0.001 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 161 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.5941 (tpp) cc_final: 0.5546 (tpp) REVERT: A 165 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7348 (mm-40) REVERT: B 295 MET cc_start: 0.7371 (mmm) cc_final: 0.6811 (mtt) REVERT: C 7 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8692 (tt) REVERT: C 43 ASP cc_start: 0.6602 (t70) cc_final: 0.6329 (t0) REVERT: E 118 LEU cc_start: 0.4405 (mm) cc_final: 0.3447 (mm) REVERT: E 125 GLN cc_start: 0.0888 (OUTLIER) cc_final: -0.0047 (mt0) REVERT: E 130 GLU cc_start: 0.6061 (tp30) cc_final: 0.5664 (tp30) REVERT: E 139 MET cc_start: 0.7547 (tmm) cc_final: 0.7318 (tmm) REVERT: E 201 GLU cc_start: 0.7121 (tm-30) cc_final: 0.6907 (tm-30) outliers start: 60 outliers final: 55 residues processed: 207 average time/residue: 0.3352 time to fit residues: 104.9541 Evaluate side-chains 212 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 155 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 249 TYR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 220 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 ASN G 125 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20210 Z= 0.203 Angle : 0.635 12.787 27609 Z= 0.324 Chirality : 0.044 0.189 3152 Planarity : 0.005 0.049 3387 Dihedral : 14.878 141.671 3160 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.85 % Rotamer: Outliers : 2.38 % Allowed : 20.26 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.17), residues: 2370 helix: 0.77 (0.21), residues: 657 sheet: 0.32 (0.22), residues: 574 loop : -2.12 (0.17), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 381 HIS 0.012 0.001 HIS A 103 PHE 0.019 0.001 PHE E 2 TYR 0.014 0.001 TYR G 249 ARG 0.011 0.000 ARG G 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4740 Ramachandran restraints generated. 2370 Oldfield, 0 Emsley, 2370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 163 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 HIS cc_start: 0.6822 (t70) cc_final: 0.6618 (t-170) REVERT: A 161 MET cc_start: 0.5858 (tpp) cc_final: 0.5482 (tpp) REVERT: A 165 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7435 (mm-40) REVERT: B 295 MET cc_start: 0.7473 (mmm) cc_final: 0.6553 (mtt) REVERT: C 7 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8676 (tt) REVERT: C 43 ASP cc_start: 0.6611 (t70) cc_final: 0.6327 (t0) REVERT: E 118 LEU cc_start: 0.4362 (mm) cc_final: 0.3855 (mm) REVERT: E 119 MET cc_start: 0.4856 (pmm) cc_final: 0.4339 (pmm) REVERT: E 139 MET cc_start: 0.7628 (tmm) cc_final: 0.7223 (tmm) REVERT: E 201 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6803 (tm-30) outliers start: 49 outliers final: 47 residues processed: 201 average time/residue: 0.3449 time to fit residues: 104.0234 Evaluate side-chains 203 residues out of total 2074 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 155 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 727 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 CYS Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 135 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 211 TYR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 28 TRP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 191 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 196 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN E 8 GLN ** G 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.107186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.082581 restraints weight = 55870.871| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.74 r_work: 0.3342 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20210 Z= 0.207 Angle : 0.629 12.935 27609 Z= 0.321 Chirality : 0.043 0.250 3152 Planarity : 0.005 0.048 3387 Dihedral : 14.756 141.900 3160 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.58 % Allowed : 20.26 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2370 helix: 0.82 (0.21), residues: 665 sheet: 0.42 (0.22), residues: 580 loop : -2.04 (0.17), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 381 HIS 0.013 0.001 HIS A 103 PHE 0.020 0.001 PHE A 794 TYR 0.013 0.001 TYR G 211 ARG 0.011 0.000 ARG G 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4630.86 seconds wall clock time: 84 minutes 54.64 seconds (5094.64 seconds total)