Starting phenix.real_space_refine on Mon Feb 19 22:43:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3e_30555/02_2024/7d3e_30555_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3e_30555/02_2024/7d3e_30555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3e_30555/02_2024/7d3e_30555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3e_30555/02_2024/7d3e_30555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3e_30555/02_2024/7d3e_30555_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d3e_30555/02_2024/7d3e_30555_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 4 7.16 5 P 10 5.49 5 S 88 5.16 5 Na 4 4.78 5 C 16754 2.51 5 N 4448 2.21 5 O 4704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 238": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 341": "NH1" <-> "NH2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ASP 462": "OD1" <-> "OD2" Residue "A ASP 475": "OD1" <-> "OD2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A GLU 528": "OE1" <-> "OE2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1062": "NH1" <-> "NH2" Residue "A TYR 1065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1087": "NH1" <-> "NH2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1113": "NH1" <-> "NH2" Residue "A GLU 1114": "OE1" <-> "OE2" Residue "A ASP 1124": "OD1" <-> "OD2" Residue "A TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1372": "OE1" <-> "OE2" Residue "A PHE 1380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1434": "OD1" <-> "OD2" Residue "A ARG 1481": "NH1" <-> "NH2" Residue "A PHE 1493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C GLU 114": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 282": "NH1" <-> "NH2" Residue "C PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 341": "NH1" <-> "NH2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C ARG 395": "NH1" <-> "NH2" Residue "C GLU 402": "OE1" <-> "OE2" Residue "C PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 452": "OD1" <-> "OD2" Residue "C ASP 462": "OD1" <-> "OD2" Residue "C ASP 475": "OD1" <-> "OD2" Residue "C ARG 507": "NH1" <-> "NH2" Residue "C GLU 528": "OE1" <-> "OE2" Residue "C ARG 760": "NH1" <-> "NH2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 772": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 834": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 865": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1036": "NH1" <-> "NH2" Residue "C TYR 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1059": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1062": "NH1" <-> "NH2" Residue "C TYR 1065": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1087": "NH1" <-> "NH2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1113": "NH1" <-> "NH2" Residue "C GLU 1114": "OE1" <-> "OE2" Residue "C ASP 1124": "OD1" <-> "OD2" Residue "C TYR 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1372": "OE1" <-> "OE2" Residue "C PHE 1380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1434": "OD1" <-> "OD2" Residue "C ARG 1481": "NH1" <-> "NH2" Residue "C PHE 1493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D ARG 56": "NH1" <-> "NH2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 152": "OD1" <-> "OD2" Residue "D TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26012 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1380, 10545 Classifications: {'peptide': 1380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PCIS': 2, 'PTRANS': 76, 'TRANS': 1301} Chain breaks: 10 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 829 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 26, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 402 Chain: "B" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2085 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 257} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 10545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1380, 10545 Classifications: {'peptide': 1380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 174} Link IDs: {'PCIS': 2, 'PTRANS': 76, 'TRANS': 1301} Chain breaks: 10 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 655 Unresolved non-hydrogen angles: 829 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 7, 'GLU:plan': 26, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 402 Chain: "D" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2085 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 257} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 231 Unusual residues: {' NA': 2, 'FAD': 1, 'HEM': 2, 'NAG': 3, 'NDP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 231 Unusual residues: {' NA': 2, 'FAD': 1, 'HEM': 2, 'NAG': 3, 'NDP': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 13.83, per 1000 atoms: 0.53 Number of scatterers: 26012 At special positions: 0 Unit cell: (149.435, 130.625, 169.29, 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) Fe 4 26.01 S 88 16.00 P 10 15.00 Na 4 11.00 O 4704 8.00 N 4448 7.00 C 16754 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A1165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 345 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 579 " distance=2.03 Simple disulfide: pdb=" SG CYS B 167 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C1165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 345 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 579 " distance=2.03 Simple disulfide: pdb=" SG CYS D 167 " - pdb=" SG CYS D 234 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-2 " MAN E 4 " - " MAN E 5 " " MAN E 5 " - " MAN E 6 " " MAN E 8 " - " MAN E 9 " " MAN F 4 " - " MAN F 5 " " MAN F 5 " - " MAN F 6 " " MAN F 8 " - " MAN F 9 " ALPHA1-3 " BMA E 3 " - " MAN E 4 " " MAN E 7 " - " MAN E 10 " " BMA F 3 " - " MAN F 4 " " MAN F 7 " - " MAN F 10 " ALPHA1-6 " BMA E 3 " - " MAN E 7 " " MAN E 7 " - " MAN E 8 " " BMA F 3 " - " MAN F 7 " " MAN F 7 " - " MAN F 8 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG A1605 " - " ASN A 94 " " NAG A1606 " - " ASN A 534 " " NAG A1607 " - " ASN A 342 " " NAG B 501 " - " ASN B 84 " " NAG B 502 " - " ASN B 121 " " NAG C1605 " - " ASN C 94 " " NAG C1606 " - " ASN C 534 " " NAG C1607 " - " ASN C 342 " " NAG D 501 " - " ASN D 84 " " NAG D 502 " - " ASN D 121 " " NAG E 1 " - " ASN B 109 " " NAG F 1 " - " ASN D 109 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.86 Conformation dependent library (CDL) restraints added in 5.5 seconds 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 14 sheets defined 47.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.29 Creating SS restraints... Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'A' and resid 97 through 110 Processing helix chain 'A' and resid 176 through 179 No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 183 through 189 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 243 through 266 Processing helix chain 'A' and resid 272 through 293 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 320 through 333 removed outlier: 3.881A pdb=" N ALA A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 390 Processing helix chain 'A' and resid 402 through 405 No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 419 through 429 Processing helix chain 'A' and resid 435 through 441 Processing helix chain 'A' and resid 450 through 452 No H-bonds generated for 'chain 'A' and resid 450 through 452' Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 481 through 488 Processing helix chain 'A' and resid 495 through 510 Processing helix chain 'A' and resid 519 through 521 No H-bonds generated for 'chain 'A' and resid 519 through 521' Processing helix chain 'A' and resid 526 through 533 Processing helix chain 'A' and resid 537 through 545 Processing helix chain 'A' and resid 549 through 551 No H-bonds generated for 'chain 'A' and resid 549 through 551' Processing helix chain 'A' and resid 592 through 618 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 719 through 735 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 757 through 776 removed outlier: 3.731A pdb=" N THR A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N GLN A 774 " --> pdb=" O HIS A 770 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 799 Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'A' and resid 837 through 847 Processing helix chain 'A' and resid 854 through 863 Processing helix chain 'A' and resid 874 through 886 Processing helix chain 'A' and resid 892 through 903 Processing helix chain 'A' and resid 918 through 924 Processing helix chain 'A' and resid 1028 through 1068 removed outlier: 6.309A pdb=" N ARG A1043 " --> pdb=" O GLU A1039 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N HIS A1044 " --> pdb=" O ASN A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1077 No H-bonds generated for 'chain 'A' and resid 1075 through 1077' Processing helix chain 'A' and resid 1081 through 1099 Processing helix chain 'A' and resid 1101 through 1104 Processing helix chain 'A' and resid 1106 through 1112 Processing helix chain 'A' and resid 1116 through 1119 Processing helix chain 'A' and resid 1123 through 1157 removed outlier: 4.637A pdb=" N VAL A1127 " --> pdb=" O ASP A1124 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE A1138 " --> pdb=" O SER A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1166 Processing helix chain 'A' and resid 1182 through 1187 Processing helix chain 'A' and resid 1190 through 1208 Processing helix chain 'A' and resid 1211 through 1216 Processing helix chain 'A' and resid 1219 through 1238 removed outlier: 4.628A pdb=" N LEU A1227 " --> pdb=" O LEU A1223 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TYR A1228 " --> pdb=" O THR A1224 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE A1229 " --> pdb=" O HIS A1225 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LEU A1230 " --> pdb=" O HIS A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1269 removed outlier: 4.828A pdb=" N VAL A1255 " --> pdb=" O ILE A1251 " (cutoff:3.500A) Proline residue: A1256 - end of helix Processing helix chain 'A' and resid 1311 through 1313 No H-bonds generated for 'chain 'A' and resid 1311 through 1313' Processing helix chain 'A' and resid 1341 through 1351 Processing helix chain 'A' and resid 1376 through 1379 Processing helix chain 'A' and resid 1389 through 1408 removed outlier: 3.652A pdb=" N VAL A1392 " --> pdb=" O GLY A1389 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1393 " --> pdb=" O ILE A1390 " (cutoff:3.500A) Proline residue: A1394 - end of helix Processing helix chain 'A' and resid 1430 through 1442 removed outlier: 3.601A pdb=" N ASP A1434 " --> pdb=" O GLU A1430 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1460 No H-bonds generated for 'chain 'A' and resid 1458 through 1460' Processing helix chain 'A' and resid 1463 through 1473 Processing helix chain 'A' and resid 1498 through 1508 Processing helix chain 'A' and resid 1523 through 1538 Processing helix chain 'B' and resid 22 through 44 Proline residue: B 43 - end of helix Processing helix chain 'B' and resid 51 through 72 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'B' and resid 152 through 161 removed outlier: 3.807A pdb=" N PHE B 161 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 199 Processing helix chain 'B' and resid 203 through 229 Processing helix chain 'B' and resid 249 through 274 Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'C' and resid 97 through 110 Processing helix chain 'C' and resid 176 through 179 No H-bonds generated for 'chain 'C' and resid 176 through 179' Processing helix chain 'C' and resid 183 through 189 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 243 through 266 Processing helix chain 'C' and resid 272 through 293 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 320 through 333 removed outlier: 3.882A pdb=" N ALA C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N MET C 333 " --> pdb=" O PHE C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 390 Processing helix chain 'C' and resid 402 through 405 No H-bonds generated for 'chain 'C' and resid 402 through 405' Processing helix chain 'C' and resid 419 through 429 Processing helix chain 'C' and resid 435 through 441 Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 455 through 459 Processing helix chain 'C' and resid 464 through 471 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 481 through 488 Processing helix chain 'C' and resid 495 through 510 Processing helix chain 'C' and resid 519 through 521 No H-bonds generated for 'chain 'C' and resid 519 through 521' Processing helix chain 'C' and resid 526 through 533 Processing helix chain 'C' and resid 537 through 545 Processing helix chain 'C' and resid 549 through 551 No H-bonds generated for 'chain 'C' and resid 549 through 551' Processing helix chain 'C' and resid 592 through 618 Proline residue: C 606 - end of helix Processing helix chain 'C' and resid 719 through 735 Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 757 through 776 removed outlier: 3.725A pdb=" N THR C 766 " --> pdb=" O HIS C 762 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN C 774 " --> pdb=" O HIS C 770 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N VAL C 775 " --> pdb=" O LEU C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 799 Processing helix chain 'C' and resid 804 through 810 Processing helix chain 'C' and resid 818 through 826 Processing helix chain 'C' and resid 837 through 847 Processing helix chain 'C' and resid 854 through 863 Processing helix chain 'C' and resid 874 through 886 Processing helix chain 'C' and resid 892 through 903 Processing helix chain 'C' and resid 918 through 924 Processing helix chain 'C' and resid 1028 through 1068 removed outlier: 6.311A pdb=" N ARG C1043 " --> pdb=" O GLU C1039 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS C1044 " --> pdb=" O ASN C1040 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1077 No H-bonds generated for 'chain 'C' and resid 1075 through 1077' Processing helix chain 'C' and resid 1081 through 1099 Processing helix chain 'C' and resid 1101 through 1104 Processing helix chain 'C' and resid 1106 through 1112 Processing helix chain 'C' and resid 1116 through 1119 Processing helix chain 'C' and resid 1123 through 1157 removed outlier: 4.650A pdb=" N VAL C1127 " --> pdb=" O ASP C1124 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE C1138 " --> pdb=" O SER C1135 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1166 Processing helix chain 'C' and resid 1182 through 1187 Processing helix chain 'C' and resid 1190 through 1208 Processing helix chain 'C' and resid 1211 through 1216 Processing helix chain 'C' and resid 1219 through 1238 removed outlier: 4.595A pdb=" N LEU C1227 " --> pdb=" O LEU C1223 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N TYR C1228 " --> pdb=" O THR C1224 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE C1229 " --> pdb=" O HIS C1225 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU C1230 " --> pdb=" O HIS C1226 " (cutoff:3.500A) Processing helix chain 'C' and resid 1249 through 1269 removed outlier: 4.828A pdb=" N VAL C1255 " --> pdb=" O ILE C1251 " (cutoff:3.500A) Proline residue: C1256 - end of helix Processing helix chain 'C' and resid 1311 through 1313 No H-bonds generated for 'chain 'C' and resid 1311 through 1313' Processing helix chain 'C' and resid 1341 through 1351 Processing helix chain 'C' and resid 1376 through 1379 Processing helix chain 'C' and resid 1389 through 1408 removed outlier: 3.650A pdb=" N VAL C1392 " --> pdb=" O GLY C1389 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C1393 " --> pdb=" O ILE C1390 " (cutoff:3.500A) Proline residue: C1394 - end of helix Processing helix chain 'C' and resid 1430 through 1442 removed outlier: 3.601A pdb=" N ASP C1434 " --> pdb=" O GLU C1430 " (cutoff:3.500A) Processing helix chain 'C' and resid 1458 through 1460 No H-bonds generated for 'chain 'C' and resid 1458 through 1460' Processing helix chain 'C' and resid 1463 through 1473 Processing helix chain 'C' and resid 1498 through 1508 Processing helix chain 'C' and resid 1523 through 1538 Processing helix chain 'D' and resid 22 through 44 Proline residue: D 43 - end of helix Processing helix chain 'D' and resid 51 through 72 Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'D' and resid 152 through 161 removed outlier: 3.806A pdb=" N PHE D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 199 Processing helix chain 'D' and resid 203 through 229 Processing helix chain 'D' and resid 249 through 274 Processing sheet with id= A, first strand: chain 'A' and resid 644 through 648 removed outlier: 5.558A pdb=" N ASP A 672 " --> pdb=" O VAL A 677 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL A 677 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 741 through 744 removed outlier: 3.626A pdb=" N ASN A 690 " --> pdb=" O LYS A 705 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1273 through 1276 Processing sheet with id= D, first strand: chain 'A' and resid 1331 through 1337 removed outlier: 5.785A pdb=" N GLN A1293 " --> pdb=" O VAL A1277 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL A1277 " --> pdb=" O GLN A1293 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 1543 through 1548 removed outlier: 6.328A pdb=" N VAL A1382 " --> pdb=" O GLY A1516 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE A1518 " --> pdb=" O VAL A1382 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A1384 " --> pdb=" O PHE A1518 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS A1520 " --> pdb=" O VAL A1384 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N VAL A1386 " --> pdb=" O CYS A1520 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS A1416 " --> pdb=" O SER A1383 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LEU A1385 " --> pdb=" O LYS A1416 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N TYR A1418 " --> pdb=" O LEU A1385 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N GLY A1387 " --> pdb=" O TYR A1418 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A1420 " --> pdb=" O GLY A1387 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE A1490 " --> pdb=" O ILE A1452 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE A1454 " --> pdb=" O ILE A1490 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS A1492 " --> pdb=" O ILE A1454 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 77 through 86 Processing sheet with id= G, first strand: chain 'B' and resid 236 through 238 removed outlier: 4.567A pdb=" N LEU B 236 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 644 through 648 removed outlier: 5.564A pdb=" N ASP C 672 " --> pdb=" O VAL C 677 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N VAL C 677 " --> pdb=" O ASP C 672 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 741 through 744 removed outlier: 3.626A pdb=" N ASN C 690 " --> pdb=" O LYS C 705 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 1273 through 1276 Processing sheet with id= K, first strand: chain 'C' and resid 1331 through 1337 removed outlier: 5.784A pdb=" N GLN C1293 " --> pdb=" O VAL C1277 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL C1277 " --> pdb=" O GLN C1293 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 1543 through 1548 removed outlier: 6.328A pdb=" N VAL C1382 " --> pdb=" O GLY C1516 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N PHE C1518 " --> pdb=" O VAL C1382 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL C1384 " --> pdb=" O PHE C1518 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N CYS C1520 " --> pdb=" O VAL C1384 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C1386 " --> pdb=" O CYS C1520 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS C1416 " --> pdb=" O SER C1383 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU C1385 " --> pdb=" O LYS C1416 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TYR C1418 " --> pdb=" O LEU C1385 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLY C1387 " --> pdb=" O TYR C1418 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C1420 " --> pdb=" O GLY C1387 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE C1490 " --> pdb=" O ILE C1452 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N ILE C1454 " --> pdb=" O ILE C1490 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS C1492 " --> pdb=" O ILE C1454 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 77 through 86 Processing sheet with id= N, first strand: chain 'D' and resid 236 through 238 removed outlier: 4.567A pdb=" N LEU D 236 " --> pdb=" O LEU D 243 " (cutoff:3.500A) 1200 hydrogen bonds defined for protein. 3276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.16 Time building geometry restraints manager: 12.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 10993 1.39 - 1.56: 15585 1.56 - 1.73: 20 1.73 - 1.90: 132 1.90 - 2.07: 16 Bond restraints: 26746 Sorted by residual: bond pdb=" O2B NDP C1603 " pdb=" P2B NDP C1603 " ideal model delta sigma weight residual 1.833 1.610 0.223 3.80e-02 6.93e+02 3.45e+01 bond pdb=" O2B NDP A1603 " pdb=" P2B NDP A1603 " ideal model delta sigma weight residual 1.833 1.610 0.223 3.80e-02 6.93e+02 3.43e+01 bond pdb=" O5D NDP C1603 " pdb=" PN NDP C1603 " ideal model delta sigma weight residual 1.757 1.608 0.149 3.50e-02 8.16e+02 1.81e+01 bond pdb=" O5D NDP A1603 " pdb=" PN NDP A1603 " ideal model delta sigma weight residual 1.757 1.608 0.149 3.50e-02 8.16e+02 1.81e+01 bond pdb=" C4A FAD C1604 " pdb=" C5A FAD C1604 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 26741 not shown) Histogram of bond angle deviations from ideal: 88.97 - 106.93: 1006 106.93 - 124.89: 34821 124.89 - 142.85: 725 142.85 - 160.81: 0 160.81 - 178.77: 8 Bond angle restraints: 36560 Sorted by residual: angle pdb=" C5B NDP A1603 " pdb=" O5B NDP A1603 " pdb=" PA NDP A1603 " ideal model delta sigma weight residual 103.84 119.19 -15.35 1.91e+00 2.73e-01 6.42e+01 angle pdb=" C5B NDP C1603 " pdb=" O5B NDP C1603 " pdb=" PA NDP C1603 " ideal model delta sigma weight residual 103.84 119.12 -15.28 1.91e+00 2.73e-01 6.37e+01 angle pdb=" PA NDP A1603 " pdb=" O3 NDP A1603 " pdb=" PN NDP A1603 " ideal model delta sigma weight residual 107.74 120.32 -12.58 1.95e+00 2.62e-01 4.14e+01 angle pdb=" PA NDP C1603 " pdb=" O3 NDP C1603 " pdb=" PN NDP C1603 " ideal model delta sigma weight residual 107.74 120.26 -12.52 1.95e+00 2.62e-01 4.11e+01 angle pdb=" C5D NDP A1603 " pdb=" O5D NDP A1603 " pdb=" PN NDP A1603 " ideal model delta sigma weight residual 104.93 119.56 -14.63 2.66e+00 1.41e-01 3.03e+01 ... (remaining 36555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.55: 15163 22.55 - 45.10: 549 45.10 - 67.66: 71 67.66 - 90.21: 57 90.21 - 112.76: 26 Dihedral angle restraints: 15866 sinusoidal: 6304 harmonic: 9562 Sorted by residual: dihedral pdb=" CA HIS A1018 " pdb=" C HIS A1018 " pdb=" N ARG A1019 " pdb=" CA ARG A1019 " ideal model delta harmonic sigma weight residual -180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA HIS C1018 " pdb=" C HIS C1018 " pdb=" N ARG C1019 " pdb=" CA ARG C1019 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C5B NDP A1603 " pdb=" O5B NDP A1603 " pdb=" PA NDP A1603 " pdb=" O3 NDP A1603 " ideal model delta sinusoidal sigma weight residual 175.04 62.28 112.76 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 15863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3562 0.060 - 0.120: 530 0.120 - 0.181: 31 0.181 - 0.241: 5 0.241 - 0.301: 2 Chirality restraints: 4130 Sorted by residual: chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 109 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 4127 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A1361 " 0.034 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A1362 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A1362 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1362 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C1361 " -0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO C1362 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO C1362 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C1362 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 55 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO C 56 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 56 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 56 " -0.024 5.00e-02 4.00e+02 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 301 2.58 - 3.16: 22060 3.16 - 3.74: 43705 3.74 - 4.32: 59929 4.32 - 4.90: 97279 Nonbonded interactions: 223274 Sorted by model distance: nonbonded pdb=" NE2 HIS A1225 " pdb="FE HEM A1601 " model vdw 2.000 3.080 nonbonded pdb=" NE2 HIS A1144 " pdb="FE HEM A1602 " model vdw 2.000 3.080 nonbonded pdb=" OH TYR D 87 " pdb=" OH TYR D 126 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR B 87 " pdb=" OH TYR B 126 " model vdw 2.219 2.440 nonbonded pdb=" OG SER C1482 " pdb=" OG1 THR C1485 " model vdw 2.226 2.440 ... (remaining 223269 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 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.770 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 72.520 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.180 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:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.223 26746 Z= 0.312 Angle : 0.678 15.348 36560 Z= 0.333 Chirality : 0.042 0.301 4130 Planarity : 0.004 0.053 4604 Dihedral : 13.631 112.760 9666 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.44 % Allowed : 2.51 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3256 helix: 1.33 (0.13), residues: 1596 sheet: -0.76 (0.26), residues: 352 loop : 0.17 (0.19), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 252 HIS 0.004 0.001 HIS C1130 PHE 0.021 0.001 PHE C 329 TYR 0.010 0.001 TYR C 435 ARG 0.004 0.000 ARG C1080 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 632 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9200 (mmm) cc_final: 0.8882 (mmm) REVERT: A 154 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8753 (mt-10) REVERT: A 164 ASP cc_start: 0.8737 (m-30) cc_final: 0.8413 (m-30) REVERT: A 210 GLN cc_start: 0.8094 (mp10) cc_final: 0.7881 (pm20) REVERT: A 225 GLN cc_start: 0.8354 (tp-100) cc_final: 0.8001 (tt0) REVERT: A 242 GLU cc_start: 0.9105 (pt0) cc_final: 0.8901 (pt0) REVERT: A 466 GLU cc_start: 0.9107 (mp0) cc_final: 0.8895 (mp0) REVERT: A 503 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 569 ARG cc_start: 0.8494 (ptp90) cc_final: 0.8173 (ptp90) REVERT: A 806 GLU cc_start: 0.9102 (tp30) cc_final: 0.8542 (tp30) REVERT: A 809 GLU cc_start: 0.8894 (tp30) cc_final: 0.8488 (tp30) REVERT: A 817 ASP cc_start: 0.8832 (t0) cc_final: 0.8261 (t0) REVERT: A 1025 SER cc_start: 0.9170 (m) cc_final: 0.8802 (t) REVERT: A 1029 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8482 (tm-30) REVERT: A 1032 GLN cc_start: 0.9336 (tp-100) cc_final: 0.9123 (tm-30) REVERT: A 1033 GLN cc_start: 0.9051 (mm110) cc_final: 0.8506 (mm-40) REVERT: A 1042 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8147 (ttm170) REVERT: A 1061 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 1119 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8309 (tpt-90) REVERT: A 1211 HIS cc_start: 0.7686 (t70) cc_final: 0.7252 (t-90) REVERT: A 1215 ARG cc_start: 0.7778 (mtm180) cc_final: 0.7519 (mtp85) REVERT: A 1372 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 1441 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8599 (tm-30) REVERT: A 1474 HIS cc_start: 0.9053 (m90) cc_final: 0.8739 (m-70) REVERT: A 1499 GLU cc_start: 0.8585 (pp20) cc_final: 0.8049 (tm-30) REVERT: A 1530 GLU cc_start: 0.8389 (tt0) cc_final: 0.8142 (tt0) REVERT: A 1535 LEU cc_start: 0.9427 (tt) cc_final: 0.9172 (tt) REVERT: A 1548 TYR cc_start: 0.7386 (m-80) cc_final: 0.6772 (m-10) REVERT: B 37 THR cc_start: 0.8866 (m) cc_final: 0.8482 (t) REVERT: B 80 GLN cc_start: 0.9183 (tt0) cc_final: 0.8976 (tt0) REVERT: B 129 GLU cc_start: 0.9001 (tt0) cc_final: 0.8797 (tt0) REVERT: B 260 LEU cc_start: 0.8801 (tt) cc_final: 0.8471 (tm) REVERT: C 40 MET cc_start: 0.9195 (mmm) cc_final: 0.8913 (mmm) REVERT: C 43 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8675 (mmm160) REVERT: C 154 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8735 (mt-10) REVERT: C 164 ASP cc_start: 0.8707 (m-30) cc_final: 0.8383 (m-30) REVERT: C 210 GLN cc_start: 0.8116 (mp10) cc_final: 0.7884 (pm20) REVERT: C 225 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7977 (tt0) REVERT: C 466 GLU cc_start: 0.9110 (mp0) cc_final: 0.8745 (mp0) REVERT: C 503 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8141 (tm-30) REVERT: C 569 ARG cc_start: 0.8509 (ptp90) cc_final: 0.8299 (ptp90) REVERT: C 806 GLU cc_start: 0.9108 (tp30) cc_final: 0.8545 (tp30) REVERT: C 809 GLU cc_start: 0.8890 (tp30) cc_final: 0.8464 (tp30) REVERT: C 817 ASP cc_start: 0.8811 (t0) cc_final: 0.8271 (t0) REVERT: C 1025 SER cc_start: 0.9181 (m) cc_final: 0.8816 (t) REVERT: C 1029 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8462 (tm-30) REVERT: C 1033 GLN cc_start: 0.9045 (mm110) cc_final: 0.8397 (mm-40) REVERT: C 1042 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8146 (ttm170) REVERT: C 1119 ARG cc_start: 0.8548 (mmm-85) cc_final: 0.8306 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7738 (t70) cc_final: 0.7301 (t-90) REVERT: C 1215 ARG cc_start: 0.7828 (mtm180) cc_final: 0.7571 (mtp85) REVERT: C 1237 ILE cc_start: 0.9140 (mt) cc_final: 0.8805 (mp) REVERT: C 1372 GLU cc_start: 0.8100 (tm-30) cc_final: 0.7287 (tm-30) REVERT: C 1374 HIS cc_start: 0.7792 (m170) cc_final: 0.7039 (m170) REVERT: C 1427 ARG cc_start: 0.9057 (ttp80) cc_final: 0.8805 (ptm160) REVERT: C 1441 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8662 (tm-30) REVERT: C 1459 GLU cc_start: 0.9223 (mp0) cc_final: 0.8819 (pt0) REVERT: C 1474 HIS cc_start: 0.9090 (m90) cc_final: 0.8784 (m-70) REVERT: C 1481 ARG cc_start: 0.8890 (mpt-90) cc_final: 0.8595 (mpt-90) REVERT: C 1499 GLU cc_start: 0.8598 (pp20) cc_final: 0.8050 (tm-30) REVERT: C 1535 LEU cc_start: 0.9451 (tt) cc_final: 0.9184 (tt) REVERT: C 1548 TYR cc_start: 0.7373 (m-80) cc_final: 0.6798 (m-10) REVERT: D 37 THR cc_start: 0.8890 (m) cc_final: 0.8549 (t) REVERT: D 80 GLN cc_start: 0.9193 (tt0) cc_final: 0.8977 (tt0) REVERT: D 129 GLU cc_start: 0.8999 (tt0) cc_final: 0.8792 (tt0) REVERT: D 260 LEU cc_start: 0.8764 (tt) cc_final: 0.8447 (tm) outliers start: 11 outliers final: 2 residues processed: 636 average time/residue: 1.2947 time to fit residues: 960.3367 Evaluate side-chains 485 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 483 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain C residue 1255 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 10.0000 chunk 250 optimal weight: 50.0000 chunk 138 optimal weight: 0.0040 chunk 85 optimal weight: 50.0000 chunk 168 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 299 optimal weight: 0.0010 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1040 ASN A1245 GLN A1506 GLN A1543 HIS C1032 GLN C1040 ASN C1245 GLN C1506 GLN C1543 HIS ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 26746 Z= 0.265 Angle : 0.597 16.914 36560 Z= 0.275 Chirality : 0.042 0.213 4130 Planarity : 0.004 0.044 4604 Dihedral : 10.951 113.998 4318 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.31 % Allowed : 11.80 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3256 helix: 1.41 (0.13), residues: 1586 sheet: -0.68 (0.26), residues: 352 loop : 0.18 (0.19), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1342 HIS 0.005 0.001 HIS C1144 PHE 0.020 0.002 PHE C 767 TYR 0.011 0.001 TYR A 310 ARG 0.010 0.001 ARG C 804 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 512 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.9115 (mmm) cc_final: 0.8840 (mmm) REVERT: A 154 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8752 (mt-10) REVERT: A 164 ASP cc_start: 0.8719 (m-30) cc_final: 0.8392 (m-30) REVERT: A 208 ASP cc_start: 0.8455 (m-30) cc_final: 0.8070 (m-30) REVERT: A 225 GLN cc_start: 0.8393 (tp-100) cc_final: 0.8077 (tt0) REVERT: A 242 GLU cc_start: 0.9135 (pt0) cc_final: 0.8906 (pt0) REVERT: A 503 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 604 CYS cc_start: 0.8550 (m) cc_final: 0.8040 (p) REVERT: A 806 GLU cc_start: 0.9161 (tp30) cc_final: 0.8954 (tp30) REVERT: A 814 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8541 (mmmm) REVERT: A 817 ASP cc_start: 0.8861 (t0) cc_final: 0.8259 (t0) REVERT: A 862 MET cc_start: 0.9230 (tmm) cc_final: 0.8885 (tmm) REVERT: A 1025 SER cc_start: 0.9161 (m) cc_final: 0.8828 (t) REVERT: A 1029 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8575 (tm-30) REVERT: A 1032 GLN cc_start: 0.9366 (tp-100) cc_final: 0.9146 (tm-30) REVERT: A 1033 GLN cc_start: 0.9052 (mm110) cc_final: 0.8490 (mm-40) REVERT: A 1042 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8293 (ttm170) REVERT: A 1119 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8212 (tpt170) REVERT: A 1211 HIS cc_start: 0.7748 (t70) cc_final: 0.7333 (t-90) REVERT: A 1215 ARG cc_start: 0.7788 (mtm180) cc_final: 0.7523 (mtp85) REVERT: A 1245 GLN cc_start: 0.8340 (mt0) cc_final: 0.8018 (mt0) REVERT: A 1372 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7574 (tm-30) REVERT: A 1441 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8645 (tm-30) REVERT: A 1459 GLU cc_start: 0.9259 (mp0) cc_final: 0.8874 (pt0) REVERT: A 1474 HIS cc_start: 0.9088 (m90) cc_final: 0.8731 (m-70) REVERT: A 1499 GLU cc_start: 0.8628 (pp20) cc_final: 0.8082 (tm-30) REVERT: A 1548 TYR cc_start: 0.7687 (m-80) cc_final: 0.7041 (m-10) REVERT: B 29 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6834 (mpp) REVERT: B 129 GLU cc_start: 0.9030 (tt0) cc_final: 0.8814 (tt0) REVERT: B 260 LEU cc_start: 0.8794 (tt) cc_final: 0.8440 (tm) REVERT: C 43 ARG cc_start: 0.8927 (mtp85) cc_final: 0.8697 (mmm160) REVERT: C 154 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8744 (mt-10) REVERT: C 164 ASP cc_start: 0.8704 (m-30) cc_final: 0.8381 (m-30) REVERT: C 208 ASP cc_start: 0.8414 (m-30) cc_final: 0.8000 (m-30) REVERT: C 225 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8025 (tt0) REVERT: C 466 GLU cc_start: 0.9122 (mp0) cc_final: 0.8728 (mp0) REVERT: C 503 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 569 ARG cc_start: 0.8422 (ptp90) cc_final: 0.8218 (ptp90) REVERT: C 604 CYS cc_start: 0.8611 (m) cc_final: 0.8124 (p) REVERT: C 806 GLU cc_start: 0.9164 (tp30) cc_final: 0.8936 (tp30) REVERT: C 814 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8524 (mmmm) REVERT: C 817 ASP cc_start: 0.8860 (t0) cc_final: 0.8285 (t0) REVERT: C 1025 SER cc_start: 0.9187 (m) cc_final: 0.8834 (t) REVERT: C 1029 GLN cc_start: 0.8896 (tm-30) cc_final: 0.8486 (tm-30) REVERT: C 1032 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8786 (tm-30) REVERT: C 1033 GLN cc_start: 0.8961 (mm110) cc_final: 0.8543 (mm-40) REVERT: C 1042 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8270 (ttm170) REVERT: C 1087 ARG cc_start: 0.8388 (mmm160) cc_final: 0.8175 (mmm160) REVERT: C 1119 ARG cc_start: 0.8607 (mmm-85) cc_final: 0.8282 (tpt170) REVERT: C 1211 HIS cc_start: 0.7796 (t70) cc_final: 0.7378 (t-90) REVERT: C 1215 ARG cc_start: 0.7837 (mtm180) cc_final: 0.7577 (mtp85) REVERT: C 1237 ILE cc_start: 0.9147 (mt) cc_final: 0.8837 (mp) REVERT: C 1245 GLN cc_start: 0.8363 (mt0) cc_final: 0.8085 (mt0) REVERT: C 1372 GLU cc_start: 0.8067 (tm-30) cc_final: 0.7617 (tm-30) REVERT: C 1427 ARG cc_start: 0.9026 (ttp80) cc_final: 0.8824 (ptm160) REVERT: C 1441 GLU cc_start: 0.8953 (tm-30) cc_final: 0.8680 (tm-30) REVERT: C 1459 GLU cc_start: 0.9190 (mp0) cc_final: 0.8856 (pt0) REVERT: C 1474 HIS cc_start: 0.9114 (m90) cc_final: 0.8754 (m-70) REVERT: C 1481 ARG cc_start: 0.9036 (mpt-90) cc_final: 0.8815 (mpp80) REVERT: C 1499 GLU cc_start: 0.8633 (pp20) cc_final: 0.8098 (tm-30) REVERT: C 1548 TYR cc_start: 0.7614 (m-80) cc_final: 0.7136 (m-10) REVERT: D 50 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6628 (ttm170) REVERT: D 129 GLU cc_start: 0.9032 (tt0) cc_final: 0.8821 (tt0) REVERT: D 226 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8385 (mmp) REVERT: D 260 LEU cc_start: 0.8795 (tt) cc_final: 0.8439 (tm) outliers start: 58 outliers final: 21 residues processed: 530 average time/residue: 1.2985 time to fit residues: 805.9126 Evaluate side-chains 512 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 486 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain B residue 29 MET Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 1018 HIS Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1382 VAL Chi-restraints excluded: chain C residue 1480 ASN Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 226 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 82 optimal weight: 50.0000 chunk 300 optimal weight: 8.9990 chunk 324 optimal weight: 2.9990 chunk 267 optimal weight: 3.9990 chunk 297 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A1509 HIS A1543 HIS C1509 HIS C1543 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26746 Z= 0.179 Angle : 0.559 12.533 36560 Z= 0.263 Chirality : 0.040 0.223 4130 Planarity : 0.004 0.044 4604 Dihedral : 10.433 111.129 4318 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.99 % Allowed : 13.36 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 3256 helix: 1.47 (0.13), residues: 1576 sheet: -0.65 (0.25), residues: 352 loop : 0.15 (0.19), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1342 HIS 0.003 0.001 HIS A 256 PHE 0.014 0.001 PHE A 253 TYR 0.013 0.001 TYR A1099 ARG 0.012 0.000 ARG C 804 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 524 time to evaluate : 2.853 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: A 40 MET cc_start: 0.9172 (mmm) cc_final: 0.8845 (mmm) REVERT: A 154 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8843 (mm-30) REVERT: A 164 ASP cc_start: 0.8633 (m-30) cc_final: 0.8420 (m-30) REVERT: A 225 GLN cc_start: 0.8373 (tp-100) cc_final: 0.8078 (tt0) REVERT: A 329 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8868 (p90) REVERT: A 461 ASN cc_start: 0.8887 (p0) cc_final: 0.8634 (p0) REVERT: A 503 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 604 CYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 806 GLU cc_start: 0.9136 (tp30) cc_final: 0.8895 (tp30) REVERT: A 814 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8550 (mmmm) REVERT: A 817 ASP cc_start: 0.8904 (t0) cc_final: 0.8367 (t0) REVERT: A 1025 SER cc_start: 0.9155 (m) cc_final: 0.8837 (p) REVERT: A 1029 GLN cc_start: 0.9037 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 1032 GLN cc_start: 0.9354 (tp-100) cc_final: 0.9147 (tm-30) REVERT: A 1033 GLN cc_start: 0.9046 (mm110) cc_final: 0.8496 (mm-40) REVERT: A 1042 ARG cc_start: 0.8693 (ttp80) cc_final: 0.8266 (ttm170) REVERT: A 1119 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8292 (tpt-90) REVERT: A 1211 HIS cc_start: 0.7738 (t70) cc_final: 0.7314 (t-90) REVERT: A 1215 ARG cc_start: 0.7786 (mtm180) cc_final: 0.7514 (mtp85) REVERT: A 1293 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7538 (pt0) REVERT: A 1315 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7754 (m) REVERT: A 1372 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7404 (tm-30) REVERT: A 1441 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 1459 GLU cc_start: 0.9253 (mp0) cc_final: 0.8875 (pt0) REVERT: A 1474 HIS cc_start: 0.9062 (m90) cc_final: 0.8672 (m-70) REVERT: A 1499 GLU cc_start: 0.8597 (pp20) cc_final: 0.8041 (tm-30) REVERT: A 1513 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.8580 (mmm-85) REVERT: A 1548 TYR cc_start: 0.7619 (m-80) cc_final: 0.7137 (m-10) REVERT: B 260 LEU cc_start: 0.8818 (tt) cc_final: 0.8443 (tm) REVERT: C 43 ARG cc_start: 0.8929 (mtp85) cc_final: 0.8676 (mmm160) REVERT: C 154 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8842 (mm-30) REVERT: C 164 ASP cc_start: 0.8705 (m-30) cc_final: 0.8385 (m-30) REVERT: C 225 GLN cc_start: 0.8360 (tp-100) cc_final: 0.8058 (tt0) REVERT: C 329 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8891 (p90) REVERT: C 466 GLU cc_start: 0.9125 (mp0) cc_final: 0.8703 (mp0) REVERT: C 503 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 569 ARG cc_start: 0.8466 (ptp90) cc_final: 0.8240 (ptp90) REVERT: C 604 CYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8193 (p) REVERT: C 804 ARG cc_start: 0.8671 (ttm110) cc_final: 0.8135 (ttm110) REVERT: C 814 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8569 (mmmm) REVERT: C 817 ASP cc_start: 0.8929 (t0) cc_final: 0.8353 (t0) REVERT: C 1025 SER cc_start: 0.9149 (m) cc_final: 0.8835 (p) REVERT: C 1029 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8513 (tm-30) REVERT: C 1032 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8815 (tm-30) REVERT: C 1033 GLN cc_start: 0.8987 (mm110) cc_final: 0.8548 (mm-40) REVERT: C 1042 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8383 (ptp-170) REVERT: C 1119 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.8255 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7783 (t70) cc_final: 0.7360 (t-90) REVERT: C 1215 ARG cc_start: 0.7862 (mtm180) cc_final: 0.7593 (mtp85) REVERT: C 1237 ILE cc_start: 0.9152 (mt) cc_final: 0.8830 (mp) REVERT: C 1372 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7579 (tm-30) REVERT: C 1441 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8694 (tm-30) REVERT: C 1459 GLU cc_start: 0.9186 (mp0) cc_final: 0.8873 (pt0) REVERT: C 1474 HIS cc_start: 0.9063 (m90) cc_final: 0.8684 (m-70) REVERT: C 1481 ARG cc_start: 0.9041 (mpt-90) cc_final: 0.8584 (mpt-90) REVERT: C 1488 ARG cc_start: 0.9031 (ttp80) cc_final: 0.8760 (ttp80) REVERT: C 1499 GLU cc_start: 0.8610 (pp20) cc_final: 0.8032 (tm-30) REVERT: C 1513 ARG cc_start: 0.8849 (mmm-85) cc_final: 0.8593 (mmm-85) REVERT: C 1548 TYR cc_start: 0.7533 (m-80) cc_final: 0.7113 (m-10) REVERT: D 50 ARG cc_start: 0.7070 (OUTLIER) cc_final: 0.6709 (mtm180) REVERT: D 53 TRP cc_start: 0.7162 (t-100) cc_final: 0.6542 (t-100) REVERT: D 129 GLU cc_start: 0.8865 (tt0) cc_final: 0.8642 (tt0) REVERT: D 226 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8377 (mmp) REVERT: D 260 LEU cc_start: 0.8834 (tt) cc_final: 0.8475 (tm) outliers start: 75 outliers final: 24 residues processed: 554 average time/residue: 1.2504 time to fit residues: 814.1849 Evaluate side-chains 518 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 484 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 814 LYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1293 GLN Chi-restraints excluded: chain A residue 1315 THR Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 863 TYR Chi-restraints excluded: chain C residue 1018 HIS Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 226 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 20.0000 chunk 225 optimal weight: 50.0000 chunk 155 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 301 optimal weight: 20.0000 chunk 318 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 50.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 352 ASN A1040 ASN A1528 ASN A1543 HIS C 352 ASN C1506 GLN C1543 HIS D 102 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 26746 Z= 0.415 Angle : 0.655 16.445 36560 Z= 0.307 Chirality : 0.044 0.244 4130 Planarity : 0.005 0.049 4604 Dihedral : 10.564 110.916 4318 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.79 % Allowed : 13.72 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3256 helix: 1.44 (0.13), residues: 1562 sheet: -0.68 (0.25), residues: 352 loop : 0.12 (0.19), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C1342 HIS 0.007 0.001 HIS C1144 PHE 0.026 0.002 PHE A 101 TYR 0.016 0.002 TYR C1099 ARG 0.011 0.001 ARG C1427 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 495 time to evaluate : 3.315 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: A 154 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8787 (mt-10) REVERT: A 164 ASP cc_start: 0.8634 (m-30) cc_final: 0.8420 (m-30) REVERT: A 225 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8118 (tt0) REVERT: A 329 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8332 (p90) REVERT: A 461 ASN cc_start: 0.8899 (p0) cc_final: 0.8668 (p0) REVERT: A 503 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8122 (tm-30) REVERT: A 527 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9116 (ttmm) REVERT: A 604 CYS cc_start: 0.8641 (m) cc_final: 0.8227 (p) REVERT: A 806 GLU cc_start: 0.9194 (tp30) cc_final: 0.8961 (tp30) REVERT: A 817 ASP cc_start: 0.8961 (t0) cc_final: 0.8392 (t0) REVERT: A 1025 SER cc_start: 0.9156 (m) cc_final: 0.8878 (p) REVERT: A 1029 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8589 (tm-30) REVERT: A 1032 GLN cc_start: 0.9389 (tp-100) cc_final: 0.9139 (tm-30) REVERT: A 1033 GLN cc_start: 0.9086 (mm110) cc_final: 0.8512 (mm-40) REVERT: A 1042 ARG cc_start: 0.8676 (ttp80) cc_final: 0.8318 (ttm170) REVERT: A 1119 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.8045 (tpt170) REVERT: A 1211 HIS cc_start: 0.7806 (t70) cc_final: 0.7416 (t-90) REVERT: A 1215 ARG cc_start: 0.7897 (mtm180) cc_final: 0.7640 (mtp85) REVERT: A 1293 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: A 1372 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 1432 LEU cc_start: 0.9234 (tm) cc_final: 0.9022 (tp) REVERT: A 1441 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8633 (tm-30) REVERT: A 1459 GLU cc_start: 0.9302 (mp0) cc_final: 0.8906 (pt0) REVERT: A 1474 HIS cc_start: 0.9177 (m90) cc_final: 0.8728 (m-70) REVERT: A 1513 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8618 (mmm-85) REVERT: A 1548 TYR cc_start: 0.7734 (m-80) cc_final: 0.7178 (m-10) REVERT: B 200 MET cc_start: 0.6991 (ttp) cc_final: 0.6530 (OUTLIER) REVERT: B 260 LEU cc_start: 0.8793 (tt) cc_final: 0.8395 (tm) REVERT: C 154 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8771 (mt-10) REVERT: C 164 ASP cc_start: 0.8708 (m-30) cc_final: 0.8393 (m-30) REVERT: C 225 GLN cc_start: 0.8416 (tp-100) cc_final: 0.8094 (tt0) REVERT: C 329 PHE cc_start: 0.9153 (OUTLIER) cc_final: 0.8349 (p90) REVERT: C 466 GLU cc_start: 0.9080 (mp0) cc_final: 0.8670 (mp0) REVERT: C 503 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8162 (tm-30) REVERT: C 527 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9124 (ttmm) REVERT: C 569 ARG cc_start: 0.8393 (ptp90) cc_final: 0.8118 (ptp90) REVERT: C 604 CYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8218 (p) REVERT: C 814 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8552 (mmmm) REVERT: C 817 ASP cc_start: 0.8967 (t0) cc_final: 0.8412 (t0) REVERT: C 1025 SER cc_start: 0.9188 (m) cc_final: 0.8917 (p) REVERT: C 1029 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8394 (tm-30) REVERT: C 1032 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8771 (tm-30) REVERT: C 1033 GLN cc_start: 0.9001 (mm110) cc_final: 0.8432 (mm-40) REVERT: C 1042 ARG cc_start: 0.8690 (ttp80) cc_final: 0.8329 (ttm170) REVERT: C 1119 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8199 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7849 (t70) cc_final: 0.7466 (t-90) REVERT: C 1215 ARG cc_start: 0.7910 (mtm180) cc_final: 0.7660 (mtp85) REVERT: C 1372 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7636 (tm-30) REVERT: C 1432 LEU cc_start: 0.9243 (tm) cc_final: 0.9028 (tp) REVERT: C 1441 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8661 (tm-30) REVERT: C 1459 GLU cc_start: 0.9295 (mp0) cc_final: 0.8887 (pt0) REVERT: C 1474 HIS cc_start: 0.9162 (m90) cc_final: 0.8713 (m-70) REVERT: C 1481 ARG cc_start: 0.9004 (mpt-90) cc_final: 0.8555 (mpt-90) REVERT: C 1513 ARG cc_start: 0.8870 (mmm-85) cc_final: 0.8508 (mmm-85) REVERT: C 1548 TYR cc_start: 0.7695 (m-80) cc_final: 0.7285 (m-10) REVERT: D 53 TRP cc_start: 0.7253 (t-100) cc_final: 0.6779 (t-100) REVERT: D 200 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6924 (ptm) REVERT: D 260 LEU cc_start: 0.8808 (tt) cc_final: 0.8419 (tm) outliers start: 95 outliers final: 42 residues processed: 534 average time/residue: 1.3244 time to fit residues: 823.5264 Evaluate side-chains 520 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 471 time to evaluate : 2.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1293 GLN Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1480 ASN Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain A residue 1542 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 863 TYR Chi-restraints excluded: chain C residue 1018 HIS Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1382 VAL Chi-restraints excluded: chain C residue 1412 VAL Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain C residue 1542 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 200 MET Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 263 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 237 optimal weight: 0.0000 chunk 131 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 286 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 376 GLN ** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 ASN A1543 HIS B 102 GLN C 328 GLN C 352 ASN C1245 GLN C1506 GLN C1543 HIS D 80 GLN D 102 GLN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26746 Z= 0.201 Angle : 0.579 11.687 36560 Z= 0.272 Chirality : 0.041 0.235 4130 Planarity : 0.004 0.048 4604 Dihedral : 10.102 109.583 4318 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.39 % Allowed : 14.47 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.15), residues: 3256 helix: 1.48 (0.13), residues: 1578 sheet: -0.67 (0.26), residues: 352 loop : 0.17 (0.19), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1342 HIS 0.004 0.001 HIS C1148 PHE 0.015 0.001 PHE C 253 TYR 0.015 0.001 TYR C1099 ARG 0.014 0.001 ARG C 804 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 508 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8736 (mt-10) REVERT: A 225 GLN cc_start: 0.8409 (tp-100) cc_final: 0.8140 (tt0) REVERT: A 229 ARG cc_start: 0.8511 (tmm160) cc_final: 0.8309 (tmm160) REVERT: A 329 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8360 (p90) REVERT: A 461 ASN cc_start: 0.8894 (p0) cc_final: 0.8656 (p0) REVERT: A 503 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 527 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9112 (ttmm) REVERT: A 604 CYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8256 (p) REVERT: A 804 ARG cc_start: 0.8649 (ttm110) cc_final: 0.8323 (ttm110) REVERT: A 806 GLU cc_start: 0.9158 (tp30) cc_final: 0.8923 (tp30) REVERT: A 817 ASP cc_start: 0.8959 (t0) cc_final: 0.8415 (t0) REVERT: A 1025 SER cc_start: 0.9125 (m) cc_final: 0.8831 (p) REVERT: A 1029 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8539 (tm-30) REVERT: A 1032 GLN cc_start: 0.9334 (tp-100) cc_final: 0.9119 (tm-30) REVERT: A 1033 GLN cc_start: 0.9056 (mm110) cc_final: 0.8577 (mm-40) REVERT: A 1042 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8076 (ttm170) REVERT: A 1119 ARG cc_start: 0.8534 (mmm-85) cc_final: 0.8238 (tpt-90) REVERT: A 1211 HIS cc_start: 0.7768 (t70) cc_final: 0.7356 (t-90) REVERT: A 1215 ARG cc_start: 0.7830 (mtm180) cc_final: 0.7560 (mtp85) REVERT: A 1296 GLN cc_start: 0.8435 (pm20) cc_final: 0.8001 (pp30) REVERT: A 1372 GLU cc_start: 0.8044 (tm-30) cc_final: 0.7558 (tm-30) REVERT: A 1441 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 1459 GLU cc_start: 0.9271 (mp0) cc_final: 0.8911 (pt0) REVERT: A 1474 HIS cc_start: 0.9115 (m90) cc_final: 0.8713 (m-70) REVERT: A 1513 ARG cc_start: 0.8836 (mmm-85) cc_final: 0.8563 (mmm-85) REVERT: A 1538 ARG cc_start: 0.9156 (mmm-85) cc_final: 0.8591 (tpm170) REVERT: A 1548 TYR cc_start: 0.7550 (m-80) cc_final: 0.7202 (m-10) REVERT: B 200 MET cc_start: 0.7176 (ttp) cc_final: 0.6923 (tmm) REVERT: B 260 LEU cc_start: 0.8799 (tt) cc_final: 0.8405 (tm) REVERT: C 154 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8736 (mt-10) REVERT: C 225 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8113 (tt0) REVERT: C 229 ARG cc_start: 0.8478 (tmm160) cc_final: 0.8213 (tmm160) REVERT: C 329 PHE cc_start: 0.9041 (OUTLIER) cc_final: 0.8360 (p90) REVERT: C 466 GLU cc_start: 0.9067 (mp0) cc_final: 0.8692 (mp0) REVERT: C 503 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8103 (tm-30) REVERT: C 527 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.9113 (ttmm) REVERT: C 569 ARG cc_start: 0.8430 (ptp90) cc_final: 0.8155 (ptp90) REVERT: C 604 CYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8314 (p) REVERT: C 804 ARG cc_start: 0.8652 (ttm110) cc_final: 0.8335 (ttm110) REVERT: C 813 LEU cc_start: 0.9219 (mt) cc_final: 0.8907 (mt) REVERT: C 814 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8516 (mmmm) REVERT: C 817 ASP cc_start: 0.8966 (t0) cc_final: 0.8360 (t0) REVERT: C 1025 SER cc_start: 0.9150 (m) cc_final: 0.8839 (p) REVERT: C 1029 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8511 (tm-30) REVERT: C 1032 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8772 (tm-30) REVERT: C 1033 GLN cc_start: 0.8977 (mm110) cc_final: 0.8560 (mm-40) REVERT: C 1042 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8070 (ttm170) REVERT: C 1119 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8163 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7806 (t70) cc_final: 0.7395 (t-90) REVERT: C 1215 ARG cc_start: 0.7888 (mtm180) cc_final: 0.7619 (mtp85) REVERT: C 1237 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8809 (mp) REVERT: C 1372 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7528 (tm-30) REVERT: C 1441 GLU cc_start: 0.8883 (tm-30) cc_final: 0.8642 (tm-30) REVERT: C 1459 GLU cc_start: 0.9286 (mp0) cc_final: 0.8917 (pt0) REVERT: C 1474 HIS cc_start: 0.9112 (m90) cc_final: 0.8715 (m-70) REVERT: C 1481 ARG cc_start: 0.9004 (mpt-90) cc_final: 0.8520 (mpt-90) REVERT: C 1513 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8558 (mmm-85) REVERT: C 1530 GLU cc_start: 0.8483 (tt0) cc_final: 0.8148 (tt0) REVERT: C 1538 ARG cc_start: 0.9167 (mmm-85) cc_final: 0.8581 (tpm170) REVERT: C 1548 TYR cc_start: 0.7450 (m-80) cc_final: 0.7156 (m-10) REVERT: D 129 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8815 (tt0) REVERT: D 260 LEU cc_start: 0.8832 (tt) cc_final: 0.8448 (tm) outliers start: 85 outliers final: 32 residues processed: 547 average time/residue: 1.2776 time to fit residues: 818.8995 Evaluate side-chains 526 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 485 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 604 CYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 604 CYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 1018 HIS Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1237 ILE Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1382 VAL Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 209 MET Chi-restraints excluded: chain D residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.4980 chunk 287 optimal weight: 2.9990 chunk 63 optimal weight: 50.0000 chunk 187 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 319 optimal weight: 0.9990 chunk 265 optimal weight: 0.0870 chunk 147 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 167 optimal weight: 10.0000 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A 352 ASN A1040 ASN A1528 ASN B 195 ASN C1040 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26746 Z= 0.178 Angle : 0.576 9.870 36560 Z= 0.271 Chirality : 0.041 0.261 4130 Planarity : 0.004 0.043 4604 Dihedral : 9.656 106.181 4318 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.15 % Allowed : 15.99 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 3256 helix: 1.54 (0.13), residues: 1580 sheet: -0.65 (0.26), residues: 352 loop : 0.24 (0.19), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C1342 HIS 0.003 0.001 HIS C1148 PHE 0.038 0.001 PHE C1370 TYR 0.015 0.001 TYR D 173 ARG 0.013 0.001 ARG C 804 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 512 time to evaluate : 2.835 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: A 154 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8760 (mt-10) REVERT: A 225 GLN cc_start: 0.8390 (tp-100) cc_final: 0.8148 (tt0) REVERT: A 229 ARG cc_start: 0.8453 (tmm160) cc_final: 0.8142 (tmm160) REVERT: A 329 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8357 (p90) REVERT: A 503 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 527 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9117 (ttmm) REVERT: A 804 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8421 (ttm110) REVERT: A 806 GLU cc_start: 0.9138 (tp30) cc_final: 0.8892 (tp30) REVERT: A 817 ASP cc_start: 0.8970 (t0) cc_final: 0.8412 (t0) REVERT: A 1025 SER cc_start: 0.9106 (m) cc_final: 0.8860 (p) REVERT: A 1029 GLN cc_start: 0.9016 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 1032 GLN cc_start: 0.9352 (tp-100) cc_final: 0.9138 (tm-30) REVERT: A 1042 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8084 (ttm170) REVERT: A 1119 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8182 (tpt-90) REVERT: A 1211 HIS cc_start: 0.7755 (t70) cc_final: 0.7350 (t-90) REVERT: A 1215 ARG cc_start: 0.7829 (mtm180) cc_final: 0.7560 (mtp85) REVERT: A 1372 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7477 (tm-30) REVERT: A 1432 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8890 (tp) REVERT: A 1441 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8595 (tm-30) REVERT: A 1459 GLU cc_start: 0.9271 (mp0) cc_final: 0.8915 (pt0) REVERT: A 1474 HIS cc_start: 0.9106 (m90) cc_final: 0.8667 (m-70) REVERT: A 1528 ASN cc_start: 0.9424 (t0) cc_final: 0.9135 (t0) REVERT: A 1538 ARG cc_start: 0.9100 (mmm-85) cc_final: 0.8611 (tpm170) REVERT: B 53 TRP cc_start: 0.7511 (t-100) cc_final: 0.7225 (t60) REVERT: B 260 LEU cc_start: 0.8833 (tt) cc_final: 0.8438 (tm) REVERT: C 154 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8739 (mt-10) REVERT: C 225 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8119 (tt0) REVERT: C 229 ARG cc_start: 0.8458 (tmm160) cc_final: 0.8252 (tmm160) REVERT: C 329 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.8367 (p90) REVERT: C 466 GLU cc_start: 0.9081 (mp0) cc_final: 0.8729 (mp0) REVERT: C 503 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8056 (tm-30) REVERT: C 527 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9116 (ttmm) REVERT: C 569 ARG cc_start: 0.8452 (ptp90) cc_final: 0.8184 (ptp90) REVERT: C 813 LEU cc_start: 0.9211 (mt) cc_final: 0.8881 (mt) REVERT: C 814 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8473 (mmmm) REVERT: C 817 ASP cc_start: 0.8974 (t0) cc_final: 0.8356 (t0) REVERT: C 837 PHE cc_start: 0.9074 (m-80) cc_final: 0.8656 (t80) REVERT: C 1025 SER cc_start: 0.9078 (m) cc_final: 0.8836 (p) REVERT: C 1029 GLN cc_start: 0.8966 (tm-30) cc_final: 0.8558 (tm-30) REVERT: C 1042 ARG cc_start: 0.8647 (ttp80) cc_final: 0.8073 (ttm170) REVERT: C 1119 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8215 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7796 (t70) cc_final: 0.7389 (t-90) REVERT: C 1215 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7609 (mtp85) REVERT: C 1237 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8723 (mp) REVERT: C 1372 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7514 (tm-30) REVERT: C 1376 GLU cc_start: 0.8955 (mp0) cc_final: 0.8754 (mp0) REVERT: C 1441 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8590 (tm-30) REVERT: C 1459 GLU cc_start: 0.9220 (mp0) cc_final: 0.8919 (pt0) REVERT: C 1474 HIS cc_start: 0.9087 (m90) cc_final: 0.8678 (m-70) REVERT: C 1481 ARG cc_start: 0.8949 (mpt-90) cc_final: 0.8748 (mpp80) REVERT: C 1499 GLU cc_start: 0.8729 (pp20) cc_final: 0.8197 (tm-30) REVERT: C 1513 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8598 (mmm-85) REVERT: D 53 TRP cc_start: 0.7091 (t-100) cc_final: 0.6632 (t-100) REVERT: D 129 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8829 (tt0) REVERT: D 260 LEU cc_start: 0.8828 (tt) cc_final: 0.8444 (tm) outliers start: 79 outliers final: 34 residues processed: 551 average time/residue: 1.2419 time to fit residues: 804.1307 Evaluate side-chains 526 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 484 time to evaluate : 2.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain A residue 1533 CYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1237 ILE Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1382 VAL Chi-restraints excluded: chain C residue 1425 THR Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 263 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 0.4980 chunk 35 optimal weight: 0.0470 chunk 181 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 268 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 318 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 193 optimal weight: 0.4980 chunk 146 optimal weight: 5.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A1040 ASN B 195 ASN C 376 GLN C1040 ASN C1245 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26746 Z= 0.173 Angle : 0.572 9.053 36560 Z= 0.270 Chirality : 0.040 0.254 4130 Planarity : 0.004 0.061 4604 Dihedral : 9.291 102.469 4318 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.67 % Allowed : 17.19 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3256 helix: 1.58 (0.13), residues: 1582 sheet: -0.59 (0.26), residues: 352 loop : 0.30 (0.19), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP C1342 HIS 0.003 0.000 HIS A1546 PHE 0.028 0.001 PHE C1370 TYR 0.010 0.001 TYR C1066 ARG 0.019 0.001 ARG C 804 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 532 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8765 (mt-10) REVERT: A 186 SER cc_start: 0.9114 (t) cc_final: 0.8777 (p) REVERT: A 225 GLN cc_start: 0.8380 (tp-100) cc_final: 0.8150 (tt0) REVERT: A 229 ARG cc_start: 0.8452 (tmm160) cc_final: 0.8168 (tmm160) REVERT: A 329 PHE cc_start: 0.8955 (OUTLIER) cc_final: 0.8347 (p90) REVERT: A 503 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8059 (tm-30) REVERT: A 527 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9118 (ttmm) REVERT: A 804 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8362 (ttt90) REVERT: A 806 GLU cc_start: 0.9129 (tp30) cc_final: 0.8880 (tp30) REVERT: A 817 ASP cc_start: 0.8978 (t0) cc_final: 0.8434 (t0) REVERT: A 837 PHE cc_start: 0.8984 (m-80) cc_final: 0.8588 (t80) REVERT: A 1025 SER cc_start: 0.9024 (m) cc_final: 0.8811 (p) REVERT: A 1029 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8509 (tm-30) REVERT: A 1032 GLN cc_start: 0.9345 (tp-100) cc_final: 0.9137 (tm-30) REVERT: A 1042 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8098 (ttm170) REVERT: A 1119 ARG cc_start: 0.8417 (mmm-85) cc_final: 0.8151 (tpt-90) REVERT: A 1205 MET cc_start: 0.8299 (ttm) cc_final: 0.8088 (ttm) REVERT: A 1211 HIS cc_start: 0.7753 (t70) cc_final: 0.7360 (t-90) REVERT: A 1215 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7585 (mtp85) REVERT: A 1296 GLN cc_start: 0.8500 (pm20) cc_final: 0.7953 (pp30) REVERT: A 1372 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7614 (tt0) REVERT: A 1441 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8583 (tm-30) REVERT: A 1459 GLU cc_start: 0.9265 (mp0) cc_final: 0.8909 (pt0) REVERT: A 1512 VAL cc_start: 0.9341 (t) cc_final: 0.9061 (p) REVERT: A 1528 ASN cc_start: 0.9414 (t0) cc_final: 0.9023 (t0) REVERT: A 1530 GLU cc_start: 0.8424 (tt0) cc_final: 0.7682 (tt0) REVERT: A 1548 TYR cc_start: 0.7246 (m-10) cc_final: 0.6410 (m-10) REVERT: B 53 TRP cc_start: 0.7478 (t-100) cc_final: 0.7191 (t60) REVERT: B 260 LEU cc_start: 0.8819 (tt) cc_final: 0.8428 (tm) REVERT: C 154 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8751 (mt-10) REVERT: C 186 SER cc_start: 0.9115 (t) cc_final: 0.8779 (p) REVERT: C 225 GLN cc_start: 0.8364 (tp-100) cc_final: 0.8125 (tt0) REVERT: C 229 ARG cc_start: 0.8370 (tmm160) cc_final: 0.8019 (tmm160) REVERT: C 329 PHE cc_start: 0.8952 (OUTLIER) cc_final: 0.8436 (p90) REVERT: C 466 GLU cc_start: 0.9084 (mp0) cc_final: 0.8774 (mp0) REVERT: C 503 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8065 (tm-30) REVERT: C 527 LYS cc_start: 0.9344 (OUTLIER) cc_final: 0.9115 (ttmm) REVERT: C 569 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8257 (ptp90) REVERT: C 804 ARG cc_start: 0.8683 (ttm110) cc_final: 0.8296 (ttm110) REVERT: C 813 LEU cc_start: 0.9211 (mt) cc_final: 0.8889 (mt) REVERT: C 814 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8483 (mmmm) REVERT: C 817 ASP cc_start: 0.8983 (t0) cc_final: 0.8354 (t0) REVERT: C 837 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.8701 (t80) REVERT: C 1025 SER cc_start: 0.9042 (m) cc_final: 0.8827 (p) REVERT: C 1029 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8293 (tm-30) REVERT: C 1032 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8704 (pp30) REVERT: C 1042 ARG cc_start: 0.8639 (ttp80) cc_final: 0.8066 (ttm170) REVERT: C 1119 ARG cc_start: 0.8439 (mmm-85) cc_final: 0.8181 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7781 (t70) cc_final: 0.7377 (t-90) REVERT: C 1215 ARG cc_start: 0.7882 (mtm180) cc_final: 0.7610 (mtp85) REVERT: C 1237 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8693 (mp) REVERT: C 1372 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7455 (tm-30) REVERT: C 1441 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8604 (tm-30) REVERT: C 1459 GLU cc_start: 0.9217 (mp0) cc_final: 0.8915 (pt0) REVERT: C 1474 HIS cc_start: 0.9075 (m90) cc_final: 0.8643 (m-70) REVERT: C 1499 GLU cc_start: 0.8704 (pp20) cc_final: 0.8170 (tm-30) REVERT: C 1530 GLU cc_start: 0.8488 (tt0) cc_final: 0.7744 (tt0) REVERT: C 1548 TYR cc_start: 0.7184 (m-10) cc_final: 0.6372 (m-10) REVERT: D 129 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8765 (tt0) REVERT: D 260 LEU cc_start: 0.8790 (tt) cc_final: 0.8430 (tm) outliers start: 67 outliers final: 24 residues processed: 567 average time/residue: 1.2060 time to fit residues: 808.5046 Evaluate side-chains 524 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 492 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 837 PHE Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1237 ILE Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1382 VAL Chi-restraints excluded: chain C residue 1425 THR Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 129 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 189 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 62 optimal weight: 30.0000 chunk 61 optimal weight: 40.0000 chunk 202 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 250 optimal weight: 50.0000 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A1040 ASN A1245 GLN B 102 GLN C 328 GLN C 352 ASN C1040 ASN C1245 GLN D 80 GLN D 102 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 26746 Z= 0.370 Angle : 0.648 14.988 36560 Z= 0.306 Chirality : 0.043 0.244 4130 Planarity : 0.004 0.048 4604 Dihedral : 9.776 104.755 4318 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.59 % Allowed : 17.82 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.15), residues: 3256 helix: 1.58 (0.13), residues: 1566 sheet: -0.54 (0.26), residues: 352 loop : 0.15 (0.19), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C1342 HIS 0.006 0.001 HIS C1238 PHE 0.031 0.002 PHE C 767 TYR 0.014 0.002 TYR B 173 ARG 0.014 0.001 ARG C 804 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 488 time to evaluate : 2.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8775 (mt-10) REVERT: A 225 GLN cc_start: 0.8430 (tp-100) cc_final: 0.8154 (tt0) REVERT: A 229 ARG cc_start: 0.8430 (tmm160) cc_final: 0.8143 (tmm160) REVERT: A 329 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8367 (p90) REVERT: A 503 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 527 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9135 (ttmm) REVERT: A 804 ARG cc_start: 0.8733 (ttm110) cc_final: 0.8265 (ttm110) REVERT: A 806 GLU cc_start: 0.9193 (tp30) cc_final: 0.8922 (tp30) REVERT: A 817 ASP cc_start: 0.8994 (t0) cc_final: 0.8443 (t0) REVERT: A 1025 SER cc_start: 0.9055 (m) cc_final: 0.8844 (p) REVERT: A 1029 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8527 (tm-30) REVERT: A 1032 GLN cc_start: 0.9391 (tp-100) cc_final: 0.9147 (tm-30) REVERT: A 1042 ARG cc_start: 0.8683 (ttp80) cc_final: 0.8161 (ttm170) REVERT: A 1205 MET cc_start: 0.8360 (ttm) cc_final: 0.8127 (ttm) REVERT: A 1211 HIS cc_start: 0.7797 (t70) cc_final: 0.7425 (t-90) REVERT: A 1215 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7604 (mtp85) REVERT: A 1296 GLN cc_start: 0.8554 (pm20) cc_final: 0.7881 (pp30) REVERT: A 1372 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 1441 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8558 (tm-30) REVERT: A 1459 GLU cc_start: 0.9272 (mp0) cc_final: 0.8907 (pt0) REVERT: A 1512 VAL cc_start: 0.9331 (t) cc_final: 0.9068 (p) REVERT: B 260 LEU cc_start: 0.8822 (tt) cc_final: 0.8408 (tm) REVERT: C 154 GLU cc_start: 0.9203 (mm-30) cc_final: 0.8773 (mt-10) REVERT: C 225 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8129 (tt0) REVERT: C 229 ARG cc_start: 0.8437 (tmm160) cc_final: 0.8154 (tmm160) REVERT: C 329 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8390 (p90) REVERT: C 466 GLU cc_start: 0.9079 (mp0) cc_final: 0.8751 (mp0) REVERT: C 503 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8141 (tm-30) REVERT: C 527 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9133 (ttmm) REVERT: C 569 ARG cc_start: 0.8491 (ptp90) cc_final: 0.8183 (ptp90) REVERT: C 813 LEU cc_start: 0.9279 (mt) cc_final: 0.8996 (mt) REVERT: C 817 ASP cc_start: 0.9002 (t0) cc_final: 0.8341 (t0) REVERT: C 837 PHE cc_start: 0.9109 (m-80) cc_final: 0.8713 (t80) REVERT: C 1025 SER cc_start: 0.9070 (m) cc_final: 0.8863 (p) REVERT: C 1029 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8329 (tm-30) REVERT: C 1032 GLN cc_start: 0.9108 (tm-30) cc_final: 0.8644 (pp30) REVERT: C 1042 ARG cc_start: 0.8682 (ttp80) cc_final: 0.8143 (ttm170) REVERT: C 1119 ARG cc_start: 0.8506 (mmm-85) cc_final: 0.8088 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7854 (t70) cc_final: 0.7477 (t-90) REVERT: C 1215 ARG cc_start: 0.7894 (mtm180) cc_final: 0.7636 (mtp85) REVERT: C 1237 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8784 (mp) REVERT: C 1441 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8647 (tm-30) REVERT: C 1459 GLU cc_start: 0.9288 (mp0) cc_final: 0.8917 (pt0) REVERT: C 1474 HIS cc_start: 0.9137 (m90) cc_final: 0.8720 (m-70) REVERT: C 1499 GLU cc_start: 0.8778 (pp20) cc_final: 0.8175 (tm-30) REVERT: C 1548 TYR cc_start: 0.7380 (m-10) cc_final: 0.6871 (m-10) REVERT: D 53 TRP cc_start: 0.7099 (t-100) cc_final: 0.6623 (t-100) REVERT: D 129 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8859 (tt0) REVERT: D 260 LEU cc_start: 0.8800 (tt) cc_final: 0.8406 (tm) outliers start: 65 outliers final: 35 residues processed: 519 average time/residue: 1.2911 time to fit residues: 785.9593 Evaluate side-chains 513 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 472 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1237 ILE Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1382 VAL Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 263 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 296 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 232 optimal weight: 50.0000 chunk 90 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1528 ASN C 352 ASN C1040 ASN C1245 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 26746 Z= 0.447 Angle : 0.704 15.275 36560 Z= 0.333 Chirality : 0.045 0.223 4130 Planarity : 0.005 0.068 4604 Dihedral : 10.271 111.725 4318 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.71 % Allowed : 18.02 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3256 helix: 1.39 (0.13), residues: 1576 sheet: -0.52 (0.26), residues: 348 loop : 0.13 (0.19), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C1342 HIS 0.006 0.001 HIS C1238 PHE 0.029 0.002 PHE C1370 TYR 0.022 0.002 TYR A 863 ARG 0.015 0.001 ARG C 804 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 472 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8784 (mt-10) REVERT: A 225 GLN cc_start: 0.8460 (tp-100) cc_final: 0.8146 (tt0) REVERT: A 329 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8413 (p90) REVERT: A 491 ARG cc_start: 0.8450 (ttp-110) cc_final: 0.8157 (ttp-110) REVERT: A 503 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 527 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9135 (ttmm) REVERT: A 806 GLU cc_start: 0.9236 (tp30) cc_final: 0.8615 (tp30) REVERT: A 817 ASP cc_start: 0.9036 (t0) cc_final: 0.8382 (t0) REVERT: A 837 PHE cc_start: 0.9124 (m-80) cc_final: 0.8809 (t80) REVERT: A 1025 SER cc_start: 0.9091 (m) cc_final: 0.8870 (p) REVERT: A 1029 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8576 (tm-30) REVERT: A 1032 GLN cc_start: 0.9403 (tp-100) cc_final: 0.9151 (tm-30) REVERT: A 1033 GLN cc_start: 0.9045 (mm110) cc_final: 0.8489 (mm-40) REVERT: A 1042 ARG cc_start: 0.8689 (ttp80) cc_final: 0.8133 (ttm170) REVERT: A 1116 PHE cc_start: 0.8742 (p90) cc_final: 0.8506 (p90) REVERT: A 1205 MET cc_start: 0.8399 (ttm) cc_final: 0.8091 (ttm) REVERT: A 1211 HIS cc_start: 0.7720 (t70) cc_final: 0.7351 (t-90) REVERT: A 1215 ARG cc_start: 0.7901 (mtm180) cc_final: 0.7637 (mtp85) REVERT: A 1372 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7462 (tm-30) REVERT: A 1441 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8481 (tm-30) REVERT: A 1459 GLU cc_start: 0.9275 (mp0) cc_final: 0.8921 (pt0) REVERT: B 129 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8913 (tt0) REVERT: B 260 LEU cc_start: 0.8824 (tt) cc_final: 0.8399 (tm) REVERT: C 154 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8784 (mt-10) REVERT: C 225 GLN cc_start: 0.8454 (tp-100) cc_final: 0.8146 (tt0) REVERT: C 329 PHE cc_start: 0.9146 (OUTLIER) cc_final: 0.8514 (p90) REVERT: C 466 GLU cc_start: 0.9073 (mp0) cc_final: 0.8672 (mp0) REVERT: C 491 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.8200 (ttp-110) REVERT: C 503 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8210 (tm-30) REVERT: C 527 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.9139 (ttmm) REVERT: C 569 ARG cc_start: 0.8444 (ptp90) cc_final: 0.8128 (ptp90) REVERT: C 813 LEU cc_start: 0.9295 (mt) cc_final: 0.9021 (mt) REVERT: C 817 ASP cc_start: 0.9006 (t0) cc_final: 0.8349 (t0) REVERT: C 837 PHE cc_start: 0.9149 (m-80) cc_final: 0.8705 (t80) REVERT: C 1025 SER cc_start: 0.9096 (m) cc_final: 0.8856 (p) REVERT: C 1029 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8367 (tm-30) REVERT: C 1032 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8744 (pp30) REVERT: C 1042 ARG cc_start: 0.8727 (ttp80) cc_final: 0.8178 (ttm170) REVERT: C 1116 PHE cc_start: 0.8762 (p90) cc_final: 0.8556 (p90) REVERT: C 1119 ARG cc_start: 0.8512 (mmm-85) cc_final: 0.8115 (tpt-90) REVERT: C 1211 HIS cc_start: 0.7756 (t70) cc_final: 0.7377 (t-90) REVERT: C 1215 ARG cc_start: 0.7909 (mtm180) cc_final: 0.7658 (mtp85) REVERT: C 1237 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8842 (mp) REVERT: C 1441 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8544 (tm-30) REVERT: C 1459 GLU cc_start: 0.9297 (mp0) cc_final: 0.8927 (pt0) REVERT: C 1474 HIS cc_start: 0.9184 (m90) cc_final: 0.8857 (m-70) REVERT: C 1499 GLU cc_start: 0.8806 (pp20) cc_final: 0.8265 (tm-30) REVERT: D 53 TRP cc_start: 0.7200 (t-100) cc_final: 0.6702 (t-100) REVERT: D 129 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8875 (tt0) REVERT: D 260 LEU cc_start: 0.8819 (tt) cc_final: 0.8414 (tm) outliers start: 68 outliers final: 43 residues processed: 505 average time/residue: 1.3090 time to fit residues: 771.2076 Evaluate side-chains 513 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 463 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1382 VAL Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1425 THR Chi-restraints excluded: chain A residue 1465 THR Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 129 GLU Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1128 ASP Chi-restraints excluded: chain C residue 1237 ILE Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1382 VAL Chi-restraints excluded: chain C residue 1412 VAL Chi-restraints excluded: chain C residue 1465 THR Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 263 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 0.1980 chunk 313 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 328 optimal weight: 4.9990 chunk 302 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 202 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 GLN A1528 ASN ** C1543 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26746 Z= 0.212 Angle : 0.630 10.647 36560 Z= 0.298 Chirality : 0.041 0.241 4130 Planarity : 0.004 0.063 4604 Dihedral : 9.798 112.095 4318 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.95 % Allowed : 19.26 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.15), residues: 3256 helix: 1.39 (0.13), residues: 1590 sheet: -0.61 (0.26), residues: 354 loop : 0.15 (0.19), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP A1342 HIS 0.005 0.001 HIS C1546 PHE 0.032 0.002 PHE C 767 TYR 0.021 0.001 TYR C 863 ARG 0.015 0.001 ARG C 804 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6512 Ramachandran restraints generated. 3256 Oldfield, 0 Emsley, 3256 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 491 time to evaluate : 2.949 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 154 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8764 (mt-10) REVERT: A 225 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8129 (tt0) REVERT: A 329 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8405 (p90) REVERT: A 491 ARG cc_start: 0.8389 (ttp-110) cc_final: 0.8099 (ttp-110) REVERT: A 503 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 527 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9120 (ttmm) REVERT: A 804 ARG cc_start: 0.8611 (ttm110) cc_final: 0.8216 (ttm110) REVERT: A 806 GLU cc_start: 0.9169 (tp30) cc_final: 0.8560 (tp30) REVERT: A 817 ASP cc_start: 0.8776 (t0) cc_final: 0.8419 (t70) REVERT: A 837 PHE cc_start: 0.8994 (m-80) cc_final: 0.8549 (t80) REVERT: A 1025 SER cc_start: 0.9064 (m) cc_final: 0.8844 (p) REVERT: A 1029 GLN cc_start: 0.8983 (tm-30) cc_final: 0.8462 (tm-30) REVERT: A 1032 GLN cc_start: 0.9350 (tp-100) cc_final: 0.9118 (tm-30) REVERT: A 1033 GLN cc_start: 0.9011 (mm110) cc_final: 0.8450 (mm-40) REVERT: A 1042 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8089 (ttm170) REVERT: A 1205 MET cc_start: 0.8289 (ttm) cc_final: 0.8034 (ttm) REVERT: A 1211 HIS cc_start: 0.7763 (t70) cc_final: 0.7355 (t-90) REVERT: A 1215 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7576 (mtp85) REVERT: A 1296 GLN cc_start: 0.8409 (pm20) cc_final: 0.7651 (pp30) REVERT: A 1367 ASP cc_start: 0.8524 (t0) cc_final: 0.8284 (t0) REVERT: A 1372 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7372 (tm-30) REVERT: A 1441 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8457 (tm-30) REVERT: A 1459 GLU cc_start: 0.9265 (mp0) cc_final: 0.8911 (pt0) REVERT: A 1481 ARG cc_start: 0.8600 (mpp80) cc_final: 0.8122 (mpt-90) REVERT: A 1528 ASN cc_start: 0.9392 (t0) cc_final: 0.8988 (t0) REVERT: B 53 TRP cc_start: 0.7537 (t-100) cc_final: 0.7195 (t60) REVERT: B 75 GLU cc_start: 0.9098 (tt0) cc_final: 0.8769 (tt0) REVERT: B 260 LEU cc_start: 0.8820 (tt) cc_final: 0.8409 (tm) REVERT: C 154 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8763 (mt-10) REVERT: C 186 SER cc_start: 0.9225 (t) cc_final: 0.8912 (p) REVERT: C 225 GLN cc_start: 0.8408 (tp-100) cc_final: 0.8138 (tt0) REVERT: C 329 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8416 (p90) REVERT: C 466 GLU cc_start: 0.9072 (mp0) cc_final: 0.8695 (mp0) REVERT: C 491 ARG cc_start: 0.8408 (ttp-110) cc_final: 0.8131 (ttp-110) REVERT: C 503 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 527 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9118 (ttmm) REVERT: C 569 ARG cc_start: 0.8424 (ptp90) cc_final: 0.8143 (ptp90) REVERT: C 804 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8280 (ttm110) REVERT: C 813 LEU cc_start: 0.9224 (mt) cc_final: 0.8995 (mt) REVERT: C 817 ASP cc_start: 0.9001 (t0) cc_final: 0.8320 (t0) REVERT: C 837 PHE cc_start: 0.9103 (m-80) cc_final: 0.8420 (t80) REVERT: C 1025 SER cc_start: 0.9056 (m) cc_final: 0.8848 (p) REVERT: C 1029 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8185 (tm-30) REVERT: C 1032 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8660 (pp30) REVERT: C 1042 ARG cc_start: 0.8657 (ttp80) cc_final: 0.8120 (ttm170) REVERT: C 1211 HIS cc_start: 0.7828 (t70) cc_final: 0.7424 (t-90) REVERT: C 1215 ARG cc_start: 0.7872 (mtm180) cc_final: 0.7605 (mtp85) REVERT: C 1237 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8737 (mp) REVERT: C 1441 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 1459 GLU cc_start: 0.9256 (mp0) cc_final: 0.8911 (pt0) REVERT: C 1474 HIS cc_start: 0.9127 (m90) cc_final: 0.8703 (m-70) REVERT: C 1499 GLU cc_start: 0.8739 (pp20) cc_final: 0.8150 (tm-30) REVERT: D 53 TRP cc_start: 0.7084 (t-100) cc_final: 0.6532 (t-100) REVERT: D 75 GLU cc_start: 0.9105 (tt0) cc_final: 0.8772 (tt0) REVERT: D 129 GLU cc_start: 0.9117 (OUTLIER) cc_final: 0.8818 (tt0) REVERT: D 260 LEU cc_start: 0.8792 (tt) cc_final: 0.8406 (tm) outliers start: 49 outliers final: 32 residues processed: 523 average time/residue: 1.2935 time to fit residues: 792.0182 Evaluate side-chains 505 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 467 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1124 ASP Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1407 SER Chi-restraints excluded: chain A residue 1412 VAL Chi-restraints excluded: chain A residue 1482 SER Chi-restraints excluded: chain A residue 1505 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 527 LYS Chi-restraints excluded: chain C residue 820 VAL Chi-restraints excluded: chain C residue 1078 THR Chi-restraints excluded: chain C residue 1124 ASP Chi-restraints excluded: chain C residue 1237 ILE Chi-restraints excluded: chain C residue 1243 LEU Chi-restraints excluded: chain C residue 1255 VAL Chi-restraints excluded: chain C residue 1382 VAL Chi-restraints excluded: chain C residue 1412 VAL Chi-restraints excluded: chain C residue 1465 THR Chi-restraints excluded: chain C residue 1482 SER Chi-restraints excluded: chain C residue 1505 LEU Chi-restraints excluded: chain C residue 1533 CYS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 162 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 8.9990 chunk 278 optimal weight: 0.8980 chunk 80 optimal weight: 40.0000 chunk 241 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 262 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1040 ASN A1506 GLN B 102 GLN ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1040 ASN D 80 GLN D 102 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.116582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.082821 restraints weight = 44096.817| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.11 r_work: 0.2837 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 26746 Z= 0.429 Angle : 0.696 14.850 36560 Z= 0.329 Chirality : 0.045 0.224 4130 Planarity : 0.005 0.064 4604 Dihedral : 10.200 113.823 4318 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.23 % Allowed : 19.18 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3256 helix: 1.32 (0.13), residues: 1596 sheet: -0.60 (0.26), residues: 352 loop : 0.09 (0.19), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C1342 HIS 0.005 0.001 HIS C1238 PHE 0.024 0.002 PHE A 101 TYR 0.039 0.002 TYR C1548 ARG 0.020 0.001 ARG C1119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11815.63 seconds wall clock time: 214 minutes 25.87 seconds (12865.87 seconds total)