Starting phenix.real_space_refine on Tue Aug 26 19:03:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8axv_15704/08_2025/8axv_15704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8axv_15704/08_2025/8axv_15704.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 { model { file = "/net/cci-nas-00/data/ceres_data/8axv_15704/08_2025/8axv_15704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8axv_15704/08_2025/8axv_15704.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8axv_15704/08_2025/8axv_15704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8axv_15704/08_2025/8axv_15704.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 S 324 5.16 5 C 25380 2.51 5 N 6972 2.21 5 O 7584 1.98 5 H 108 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40380 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "B" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "C" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "D" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "E" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "F" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "G" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "H" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "I" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "J" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "K" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "L" Number of atoms: 3352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 429, 3349 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 407} Chain breaks: 4 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3413 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Unusual residues: {' ZN': 1, 'MY6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1070 SG CYS A 141 187.510 120.733 31.564 1.00 88.37 S ATOM 4422 SG CYS B 141 167.166 160.687 31.536 1.00 80.35 S ATOM 7774 SG CYS C 141 129.437 185.181 31.563 1.00 82.61 S ATOM 11126 SG CYS D 141 84.483 187.511 31.563 1.00 86.70 S ATOM 14478 SG CYS E 141 44.529 167.168 31.538 1.00 79.51 S ATOM 17830 SG CYS F 141 20.036 129.436 31.560 1.00 82.22 S ATOM 21182 SG CYS G 141 17.706 84.483 31.564 1.00 87.52 S ATOM 24534 SG CYS H 141 38.048 44.523 31.538 1.00 78.23 S ATOM 27886 SG CYS I 141 75.780 20.035 31.559 1.00 82.61 S ATOM 31238 SG CYS J 141 120.732 17.706 31.564 1.00 88.07 S ATOM 34590 SG CYS K 141 160.693 38.048 31.537 1.00 78.16 S ATOM 37942 SG CYS L 141 185.183 75.780 31.561 1.00 82.57 S Time building chain proxies: 14.93, per 1000 atoms: 0.37 Number of scatterers: 40380 At special positions: 0 Unit cell: (206.394, 206.394, 83.061, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 324 16.00 O 7584 8.00 N 6972 7.00 C 25380 6.00 H 108 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.78 Conformation dependent library (CDL) restraints added in 2.5 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9792 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 48 sheets defined 33.5% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 4.089A pdb=" N LYS A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 54 Processing helix chain 'A' and resid 88 through 104 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 256 Processing helix chain 'A' and resid 335 through 347 removed outlier: 4.806A pdb=" N GLY A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 364 Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.698A pdb=" N GLN A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 469 removed outlier: 3.583A pdb=" N LYS A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 22 removed outlier: 4.106A pdb=" N LYS B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 54 Processing helix chain 'B' and resid 88 through 105 removed outlier: 4.158A pdb=" N GLY B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 335 through 347 removed outlier: 4.806A pdb=" N GLY B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE B 345 " --> pdb=" O GLN B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 364 Processing helix chain 'B' and resid 383 through 403 removed outlier: 3.736A pdb=" N GLN B 389 " --> pdb=" O PRO B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 469 removed outlier: 3.609A pdb=" N LYS B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 22 removed outlier: 4.096A pdb=" N LYS C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 54 Processing helix chain 'C' and resid 88 through 105 removed outlier: 4.122A pdb=" N GLY C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 256 Processing helix chain 'C' and resid 335 through 347 removed outlier: 4.755A pdb=" N GLY C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE C 345 " --> pdb=" O GLN C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 364 Processing helix chain 'C' and resid 383 through 403 removed outlier: 3.674A pdb=" N GLN C 389 " --> pdb=" O PRO C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 469 removed outlier: 3.561A pdb=" N LYS C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 22 removed outlier: 4.090A pdb=" N LYS D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 Processing helix chain 'D' and resid 88 through 104 Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 157 through 167 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 252 through 256 Processing helix chain 'D' and resid 335 through 347 removed outlier: 4.805A pdb=" N GLY D 344 " --> pdb=" O ASP D 340 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 Processing helix chain 'D' and resid 383 through 403 removed outlier: 3.698A pdb=" N GLN D 389 " --> pdb=" O PRO D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 469 removed outlier: 3.635A pdb=" N LYS D 469 " --> pdb=" O ARG D 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 22 removed outlier: 4.100A pdb=" N LYS E 16 " --> pdb=" O SER E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 54 Processing helix chain 'E' and resid 88 through 105 removed outlier: 4.159A pdb=" N GLY E 105 " --> pdb=" O ALA E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 256 Processing helix chain 'E' and resid 335 through 347 removed outlier: 4.807A pdb=" N GLY E 344 " --> pdb=" O ASP E 340 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ILE E 345 " --> pdb=" O GLN E 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 364 Processing helix chain 'E' and resid 383 through 403 removed outlier: 3.737A pdb=" N GLN E 389 " --> pdb=" O PRO E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 469 removed outlier: 3.586A pdb=" N LYS E 469 " --> pdb=" O ARG E 465 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 22 removed outlier: 4.095A pdb=" N LYS F 16 " --> pdb=" O SER F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 54 Processing helix chain 'F' and resid 88 through 105 removed outlier: 4.122A pdb=" N GLY F 105 " --> pdb=" O ALA F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 252 through 256 Processing helix chain 'F' and resid 335 through 347 removed outlier: 4.754A pdb=" N GLY F 344 " --> pdb=" O ASP F 340 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE F 345 " --> pdb=" O GLN F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 364 Processing helix chain 'F' and resid 383 through 403 removed outlier: 3.659A pdb=" N GLN F 389 " --> pdb=" O PRO F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 469 removed outlier: 3.564A pdb=" N LYS F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 22 removed outlier: 4.089A pdb=" N LYS G 16 " --> pdb=" O SER G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 54 Processing helix chain 'G' and resid 88 through 104 Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 256 Processing helix chain 'G' and resid 335 through 347 removed outlier: 4.804A pdb=" N GLY G 344 " --> pdb=" O ASP G 340 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE G 345 " --> pdb=" O GLN G 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 364 Processing helix chain 'G' and resid 383 through 403 removed outlier: 3.698A pdb=" N GLN G 389 " --> pdb=" O PRO G 385 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 469 removed outlier: 3.584A pdb=" N LYS G 469 " --> pdb=" O ARG G 465 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 22 removed outlier: 4.109A pdb=" N LYS H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 54 Processing helix chain 'H' and resid 88 through 105 removed outlier: 4.157A pdb=" N GLY H 105 " --> pdb=" O ALA H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 252 through 256 Processing helix chain 'H' and resid 335 through 347 removed outlier: 4.797A pdb=" N GLY H 344 " --> pdb=" O ASP H 340 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE H 345 " --> pdb=" O GLN H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 Processing helix chain 'H' and resid 383 through 403 removed outlier: 3.735A pdb=" N GLN H 389 " --> pdb=" O PRO H 385 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 469 removed outlier: 3.618A pdb=" N LYS H 469 " --> pdb=" O ARG H 465 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 22 removed outlier: 4.103A pdb=" N LYS I 16 " --> pdb=" O SER I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 54 Processing helix chain 'I' and resid 88 through 105 removed outlier: 4.122A pdb=" N GLY I 105 " --> pdb=" O ALA I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 180 through 185 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 256 Processing helix chain 'I' and resid 335 through 347 removed outlier: 4.752A pdb=" N GLY I 344 " --> pdb=" O ASP I 340 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE I 345 " --> pdb=" O GLN I 341 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 364 Processing helix chain 'I' and resid 383 through 403 removed outlier: 3.655A pdb=" N GLN I 389 " --> pdb=" O PRO I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 469 removed outlier: 3.562A pdb=" N LYS I 469 " --> pdb=" O ARG I 465 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 22 removed outlier: 4.089A pdb=" N LYS J 16 " --> pdb=" O SER J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 54 Processing helix chain 'J' and resid 88 through 104 Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'J' and resid 180 through 185 Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 252 through 256 Processing helix chain 'J' and resid 335 through 347 removed outlier: 4.805A pdb=" N GLY J 344 " --> pdb=" O ASP J 340 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ILE J 345 " --> pdb=" O GLN J 341 " (cutoff:3.500A) Processing helix chain 'J' and resid 351 through 364 Processing helix chain 'J' and resid 383 through 403 removed outlier: 3.698A pdb=" N GLN J 389 " --> pdb=" O PRO J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 469 removed outlier: 3.636A pdb=" N LYS J 469 " --> pdb=" O ARG J 465 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 22 removed outlier: 4.104A pdb=" N LYS K 16 " --> pdb=" O SER K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 54 Processing helix chain 'K' and resid 88 through 105 removed outlier: 4.155A pdb=" N GLY K 105 " --> pdb=" O ALA K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 256 Processing helix chain 'K' and resid 335 through 347 removed outlier: 4.805A pdb=" N GLY K 344 " --> pdb=" O ASP K 340 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE K 345 " --> pdb=" O GLN K 341 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 364 Processing helix chain 'K' and resid 383 through 403 removed outlier: 3.737A pdb=" N GLN K 389 " --> pdb=" O PRO K 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 469 removed outlier: 3.611A pdb=" N LYS K 469 " --> pdb=" O ARG K 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 22 removed outlier: 4.098A pdb=" N LYS L 16 " --> pdb=" O SER L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 54 Processing helix chain 'L' and resid 88 through 105 removed outlier: 4.122A pdb=" N GLY L 105 " --> pdb=" O ALA L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 125 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 252 through 256 Processing helix chain 'L' and resid 335 through 347 removed outlier: 4.755A pdb=" N GLY L 344 " --> pdb=" O ASP L 340 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE L 345 " --> pdb=" O GLN L 341 " (cutoff:3.500A) Processing helix chain 'L' and resid 351 through 364 Processing helix chain 'L' and resid 383 through 403 removed outlier: 3.670A pdb=" N GLN L 389 " --> pdb=" O PRO L 385 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 469 removed outlier: 3.559A pdb=" N LYS L 469 " --> pdb=" O ARG L 465 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 80 removed outlier: 7.009A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU A 62 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN A 151 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 176 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N PHE A 447 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N HIS A 265 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 4.437A pdb=" N TYR A 333 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.995A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 80 removed outlier: 7.009A pdb=" N ILE B 61 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU B 62 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N GLN B 151 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 176 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER B 281 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 287 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N PHE B 447 " --> pdb=" O VAL B 263 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS B 265 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 251 Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 308 removed outlier: 4.053A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 80 removed outlier: 7.012A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU C 62 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLN C 151 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 176 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N PHE C 447 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N HIS C 265 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 251 removed outlier: 4.408A pdb=" N TYR C 333 " --> pdb=" O ALA C 191 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 303 through 308 removed outlier: 4.066A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'D' and resid 78 through 80 removed outlier: 7.009A pdb=" N ILE D 61 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU D 62 " --> pdb=" O ILE D 149 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN D 151 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D 176 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER D 281 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL D 287 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N PHE D 447 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N HIS D 265 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 246 through 251 removed outlier: 4.430A pdb=" N TYR D 333 " --> pdb=" O ALA D 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 303 through 308 removed outlier: 3.995A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'E' and resid 78 through 80 removed outlier: 6.997A pdb=" N ILE E 61 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU E 62 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLN E 151 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 176 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N PHE E 447 " --> pdb=" O VAL E 263 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N HIS E 265 " --> pdb=" O PHE E 447 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 246 through 251 Processing sheet with id=AC2, first strand: chain 'E' and resid 303 through 308 removed outlier: 4.050A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'F' and resid 78 through 80 removed outlier: 7.007A pdb=" N ILE F 61 " --> pdb=" O HIS F 79 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU F 62 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N GLN F 151 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL F 176 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER F 281 " --> pdb=" O TYR F 285 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL F 287 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N PHE F 447 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS F 265 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 246 through 251 removed outlier: 4.406A pdb=" N TYR F 333 " --> pdb=" O ALA F 191 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 303 through 308 removed outlier: 4.065A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 78 through 80 removed outlier: 7.010A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU G 62 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN G 151 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL G 176 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER G 281 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL G 287 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N PHE G 447 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS G 265 " --> pdb=" O PHE G 447 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 246 through 251 removed outlier: 4.430A pdb=" N TYR G 333 " --> pdb=" O ALA G 191 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.995A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 78 through 80 removed outlier: 7.004A pdb=" N ILE H 61 " --> pdb=" O HIS H 79 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU H 62 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N GLN H 151 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL H 176 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N SER H 281 " --> pdb=" O TYR H 285 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL H 287 " --> pdb=" O VAL H 279 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N PHE H 447 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N HIS H 265 " --> pdb=" O PHE H 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 246 through 251 Processing sheet with id=AD5, first strand: chain 'H' and resid 303 through 308 removed outlier: 4.046A pdb=" N THR H 437 " --> pdb=" O HIS H 308 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 78 through 80 removed outlier: 7.015A pdb=" N ILE I 61 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU I 62 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N GLN I 151 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL I 176 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N PHE I 447 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS I 265 " --> pdb=" O PHE I 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 246 through 251 removed outlier: 4.407A pdb=" N TYR I 333 " --> pdb=" O ALA I 191 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 303 through 308 removed outlier: 4.067A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'J' and resid 78 through 80 removed outlier: 7.010A pdb=" N ILE J 61 " --> pdb=" O HIS J 79 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU J 62 " --> pdb=" O ILE J 149 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N GLN J 151 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL J 176 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER J 281 " --> pdb=" O TYR J 285 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL J 287 " --> pdb=" O VAL J 279 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N PHE J 447 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N HIS J 265 " --> pdb=" O PHE J 447 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 246 through 251 removed outlier: 4.442A pdb=" N TYR J 333 " --> pdb=" O ALA J 191 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 303 through 308 removed outlier: 3.994A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE6, first strand: chain 'K' and resid 78 through 80 removed outlier: 7.006A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU K 62 " --> pdb=" O ILE K 149 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N GLN K 151 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL K 176 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N PHE K 447 " --> pdb=" O VAL K 263 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N HIS K 265 " --> pdb=" O PHE K 447 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 246 through 251 Processing sheet with id=AE8, first strand: chain 'K' and resid 303 through 308 removed outlier: 4.044A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AF1, first strand: chain 'L' and resid 78 through 80 removed outlier: 7.012A pdb=" N ILE L 61 " --> pdb=" O HIS L 79 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU L 62 " --> pdb=" O ILE L 149 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N GLN L 151 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL L 176 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TYR L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER L 281 " --> pdb=" O TYR L 285 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL L 287 " --> pdb=" O VAL L 279 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N PHE L 447 " --> pdb=" O VAL L 263 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N HIS L 265 " --> pdb=" O PHE L 447 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 246 through 251 removed outlier: 4.408A pdb=" N TYR L 333 " --> pdb=" O ALA L 191 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 303 through 308 removed outlier: 4.074A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) 1764 hydrogen bonds defined for protein. 5100 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: 8.05 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 108 1.05 - 1.24: 5419 1.24 - 1.43: 11407 1.43 - 1.62: 23794 1.62 - 1.81: 480 Bond restraints: 41208 Sorted by residual: bond pdb=" C3 MY6 F1002 " pdb=" N2 MY6 F1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.17e+01 bond pdb=" C3 MY6 A1002 " pdb=" N2 MY6 A1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.16e+01 bond pdb=" C3 MY6 C1002 " pdb=" N2 MY6 C1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.16e+01 bond pdb=" C3 MY6 B1002 " pdb=" N2 MY6 B1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.12e+01 bond pdb=" C3 MY6 E1002 " pdb=" N2 MY6 E1002 " ideal model delta sigma weight residual 1.317 1.508 -0.191 2.00e-02 2.50e+03 9.12e+01 ... (remaining 41203 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 55293 2.03 - 4.05: 523 4.05 - 6.08: 80 6.08 - 8.11: 24 8.11 - 10.14: 24 Bond angle restraints: 55944 Sorted by residual: angle pdb=" N MET C 72 " pdb=" CA MET C 72 " pdb=" C MET C 72 " ideal model delta sigma weight residual 114.56 109.43 5.13 1.27e+00 6.20e-01 1.63e+01 angle pdb=" N MET I 72 " pdb=" CA MET I 72 " pdb=" C MET I 72 " ideal model delta sigma weight residual 114.56 109.54 5.02 1.27e+00 6.20e-01 1.56e+01 angle pdb=" N MET L 72 " pdb=" CA MET L 72 " pdb=" C MET L 72 " ideal model delta sigma weight residual 114.56 109.57 4.99 1.27e+00 6.20e-01 1.55e+01 angle pdb=" N MET F 72 " pdb=" CA MET F 72 " pdb=" C MET F 72 " ideal model delta sigma weight residual 114.56 109.98 4.58 1.27e+00 6.20e-01 1.30e+01 angle pdb=" C5 MY6 F1002 " pdb=" C6 MY6 F1002 " pdb=" N8 MY6 F1002 " ideal model delta sigma weight residual 109.68 119.82 -10.14 3.00e+00 1.11e-01 1.14e+01 ... (remaining 55939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 21226 17.72 - 35.44: 2725 35.44 - 53.16: 795 53.16 - 70.87: 177 70.87 - 88.59: 49 Dihedral angle restraints: 24972 sinusoidal: 9852 harmonic: 15120 Sorted by residual: dihedral pdb=" CA PRO I 193 " pdb=" C PRO I 193 " pdb=" N SER I 194 " pdb=" CA SER I 194 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PRO F 193 " pdb=" C PRO F 193 " pdb=" N SER F 194 " pdb=" CA SER F 194 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PRO C 193 " pdb=" C PRO C 193 " pdb=" N SER C 194 " pdb=" CA SER C 194 " ideal model delta harmonic sigma weight residual 180.00 161.44 18.56 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 24969 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3649 0.026 - 0.051: 1514 0.051 - 0.077: 596 0.077 - 0.103: 375 0.103 - 0.129: 166 Chirality restraints: 6300 Sorted by residual: chirality pdb=" CA VAL H 431 " pdb=" N VAL H 431 " pdb=" C VAL H 431 " pdb=" CB VAL H 431 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL I 305 " pdb=" N VAL I 305 " pdb=" C VAL I 305 " pdb=" CB VAL I 305 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA VAL F 305 " pdb=" N VAL F 305 " pdb=" C VAL F 305 " pdb=" CB VAL F 305 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 6297 not shown) Planarity restraints: 7104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 384 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO K 385 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO K 385 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 385 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 384 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO E 385 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO E 385 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 385 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 384 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO B 385 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " -0.023 5.00e-02 4.00e+02 ... (remaining 7101 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.48: 391 2.48 - 3.01: 25138 3.01 - 3.54: 48069 3.54 - 4.07: 75953 4.07 - 4.60: 111178 Nonbonded interactions: 260729 Sorted by model distance: nonbonded pdb=" OD1 ASP J 237 " pdb=" OG SER J 251 " model vdw 1.948 2.800 nonbonded pdb=" OD1 ASP G 237 " pdb=" OG SER G 251 " model vdw 1.950 2.800 nonbonded pdb=" OD1 ASP A 237 " pdb=" OG SER A 251 " model vdw 1.951 2.800 nonbonded pdb=" OD1 ASP D 237 " pdb=" OG SER D 251 " model vdw 1.951 2.800 nonbonded pdb=" OD1 ASP C 237 " pdb=" OG SER C 251 " model vdw 1.955 2.800 ... (remaining 260724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'B' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'C' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'D' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'E' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'F' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'G' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'H' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'I' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'J' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'K' and (resid 3 through 314 or resid 316 through 1002)) selection = (chain 'L' and (resid 3 through 314 or resid 316 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 12.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.350 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 45.060 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.007 0.191 41136 Z= 0.350 Angle : 0.568 10.136 55692 Z= 0.287 Chirality : 0.041 0.129 6300 Planarity : 0.004 0.042 7092 Dihedral : 17.869 88.594 15156 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 41.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.35 % Allowed : 30.69 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.12), residues: 5040 helix: 1.53 (0.14), residues: 1728 sheet: -0.53 (0.19), residues: 768 loop : -1.87 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 275 TYR 0.006 0.001 TYR H 382 PHE 0.017 0.001 PHE K 133 TRP 0.010 0.001 TRP H 258 HIS 0.008 0.001 HIS H 429 Details of bonding type rmsd covalent geometry : bond 0.00701 (41100) covalent geometry : angle 0.56826 (55692) hydrogen bonds : bond 0.12745 ( 1764) hydrogen bonds : angle 6.33494 ( 5100) metal coordination : bond 0.00159 ( 24) Misc. bond : bond 0.00069 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 592 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: B 136 HIS cc_start: 0.5179 (m90) cc_final: 0.4805 (m90) REVERT: C 56 ASP cc_start: 0.6244 (m-30) cc_final: 0.5738 (t70) REVERT: C 72 MET cc_start: 0.6951 (tmt) cc_final: 0.6460 (mmp) REVERT: C 149 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6209 (mp) REVERT: D 149 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6523 (mp) REVERT: D 285 TYR cc_start: 0.7123 (OUTLIER) cc_final: 0.6801 (m-80) REVERT: F 427 LYS cc_start: 0.6954 (mtpm) cc_final: 0.6391 (mtpt) REVERT: G 56 ASP cc_start: 0.5127 (t70) cc_final: 0.4766 (m-30) REVERT: L 322 ASP cc_start: 0.6498 (m-30) cc_final: 0.6287 (m-30) outliers start: 103 outliers final: 50 residues processed: 675 average time/residue: 0.4846 time to fit residues: 420.6804 Evaluate side-chains 512 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 459 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 242 SER Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 242 SER Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain H residue 242 SER Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 242 SER Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain I residue 431 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 242 SER Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 376 THR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 376 THR Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 242 SER Chi-restraints excluded: chain L residue 274 CYS Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 431 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS A 429 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 265 HIS C 356 GLN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 377 ASN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS G 429 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 164 HIS I 209 ASN ** I 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 GLN ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 265 HIS L 356 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.204498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138051 restraints weight = 66554.010| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.83 r_work: 0.3467 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 41136 Z= 0.302 Angle : 0.661 5.839 55692 Z= 0.353 Chirality : 0.049 0.331 6300 Planarity : 0.006 0.060 7092 Dihedral : 5.859 54.869 5660 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 40.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.81 % Allowed : 27.96 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.12), residues: 5040 helix: 1.50 (0.13), residues: 1728 sheet: -0.91 (0.18), residues: 804 loop : -2.17 (0.11), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 325 TYR 0.019 0.002 TYR L 195 PHE 0.027 0.003 PHE A 183 TRP 0.011 0.003 TRP H 175 HIS 0.004 0.001 HIS D 429 Details of bonding type rmsd covalent geometry : bond 0.00688 (41100) covalent geometry : angle 0.66060 (55692) hydrogen bonds : bond 0.04595 ( 1764) hydrogen bonds : angle 5.29694 ( 5100) metal coordination : bond 0.01105 ( 24) Misc. bond : bond 0.00164 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 475 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7665 (m-80) REVERT: B 123 MET cc_start: 0.7200 (mmm) cc_final: 0.6846 (mpm) REVERT: B 285 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: B 314 MET cc_start: 0.8387 (tmm) cc_final: 0.8165 (tmm) REVERT: C 56 ASP cc_start: 0.6860 (m-30) cc_final: 0.6199 (t70) REVERT: C 72 MET cc_start: 0.7203 (tmt) cc_final: 0.6581 (mmm) REVERT: D 285 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7825 (m-80) REVERT: D 441 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.6915 (mp10) REVERT: E 123 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5321 (mpm) REVERT: E 377 ASN cc_start: 0.5004 (m110) cc_final: 0.4685 (m-40) REVERT: F 72 MET cc_start: 0.4621 (mmt) cc_final: 0.4404 (tpt) REVERT: F 123 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5460 (mpm) REVERT: F 275 ARG cc_start: 0.7098 (OUTLIER) cc_final: 0.6882 (mtp85) REVERT: F 297 TYR cc_start: 0.6695 (m-10) cc_final: 0.6197 (m-10) REVERT: G 53 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: G 88 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7008 (tm-30) REVERT: G 89 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6992 (m-30) REVERT: G 184 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.8043 (mmm) REVERT: G 441 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.6863 (mp10) REVERT: H 88 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7536 (tm-30) REVERT: H 216 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7274 (m-30) REVERT: I 186 ASN cc_start: 0.8329 (t0) cc_final: 0.8125 (m-40) REVERT: J 285 TYR cc_start: 0.8137 (OUTLIER) cc_final: 0.7919 (m-80) REVERT: J 441 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: K 165 GLN cc_start: 0.6670 (mp10) cc_final: 0.6457 (mp10) REVERT: K 285 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: K 465 ARG cc_start: 0.7554 (ppp80) cc_final: 0.7248 (ppp80) REVERT: L 88 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6736 (tm-30) REVERT: L 362 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6802 (mt) outliers start: 255 outliers final: 120 residues processed: 649 average time/residue: 0.5152 time to fit residues: 425.7563 Evaluate side-chains 583 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 447 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 431 VAL Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 89 ASP Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 431 VAL Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 130 THR Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 275 ARG Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 376 THR Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 431 VAL Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 30 ARG Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 184 MET Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 301 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 242 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 301 THR Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 431 VAL Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 301 THR Chi-restraints excluded: chain I residue 431 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 242 SER Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 301 THR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 242 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 301 THR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 92 ARG Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 301 THR Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 431 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 318 optimal weight: 0.5980 chunk 405 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 317 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 314 optimal weight: 0.0670 chunk 392 optimal weight: 6.9990 chunk 417 optimal weight: 9.9990 chunk 191 optimal weight: 0.7980 chunk 160 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 164 HIS ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 377 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS E 341 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 265 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 259 HIS I 265 HIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 HIS ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 265 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.208152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.152624 restraints weight = 89745.745| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.77 r_work: 0.3537 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 36 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 41136 Z= 0.102 Angle : 0.464 5.721 55692 Z= 0.247 Chirality : 0.041 0.123 6300 Planarity : 0.004 0.052 7092 Dihedral : 5.015 54.634 5641 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 37.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.10 % Allowed : 30.42 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.12), residues: 5040 helix: 2.23 (0.14), residues: 1740 sheet: -0.85 (0.18), residues: 804 loop : -1.93 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 325 TYR 0.009 0.001 TYR L 195 PHE 0.016 0.001 PHE D 183 TRP 0.006 0.001 TRP D 258 HIS 0.004 0.001 HIS L 308 Details of bonding type rmsd covalent geometry : bond 0.00223 (41100) covalent geometry : angle 0.46382 (55692) hydrogen bonds : bond 0.02917 ( 1764) hydrogen bonds : angle 4.50472 ( 5100) metal coordination : bond 0.00247 ( 24) Misc. bond : bond 0.00084 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 480 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.7124 (mmm) cc_final: 0.6740 (mpm) REVERT: C 56 ASP cc_start: 0.6785 (m-30) cc_final: 0.6079 (t70) REVERT: C 72 MET cc_start: 0.7246 (tmt) cc_final: 0.6726 (mmm) REVERT: D 285 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.7443 (m-80) REVERT: D 441 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: E 123 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.5395 (mpm) REVERT: E 377 ASN cc_start: 0.5066 (m110) cc_final: 0.4840 (m-40) REVERT: E 441 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: F 72 MET cc_start: 0.4854 (mmt) cc_final: 0.4331 (tmt) REVERT: F 123 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5467 (mpm) REVERT: F 441 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: G 53 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: G 89 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: G 441 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: H 441 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: I 88 GLU cc_start: 0.7441 (tm-30) cc_final: 0.6865 (tm-30) REVERT: I 136 HIS cc_start: 0.5586 (m90) cc_final: 0.5028 (m90) REVERT: I 277 ASP cc_start: 0.7034 (m-30) cc_final: 0.6604 (t70) REVERT: I 297 TYR cc_start: 0.6719 (m-10) cc_final: 0.6170 (m-10) REVERT: I 441 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: J 88 GLU cc_start: 0.7368 (tm-30) cc_final: 0.7034 (tm-30) REVERT: J 136 HIS cc_start: 0.5628 (m90) cc_final: 0.4721 (m90) REVERT: J 285 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: J 441 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7014 (mp10) REVERT: K 88 GLU cc_start: 0.7445 (tm-30) cc_final: 0.7059 (tm-30) REVERT: K 165 GLN cc_start: 0.6467 (mp10) cc_final: 0.6164 (mp10) REVERT: K 285 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.7440 (m-80) REVERT: K 465 ARG cc_start: 0.7505 (ppp80) cc_final: 0.7216 (ppp80) REVERT: L 88 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6846 (tm-30) outliers start: 136 outliers final: 46 residues processed: 571 average time/residue: 0.5157 time to fit residues: 372.7362 Evaluate side-chains 512 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 452 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 392 SER Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 188 MET Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 149 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 27 optimal weight: 4.9990 chunk 468 optimal weight: 20.0000 chunk 301 optimal weight: 0.0370 chunk 105 optimal weight: 6.9990 chunk 321 optimal weight: 5.9990 chunk 464 optimal weight: 6.9990 chunk 353 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 208 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 GLN ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS D 377 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 265 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 209 ASN F 265 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 HIS ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 265 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.203568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.136552 restraints weight = 69452.774| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.32 r_work: 0.3438 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3261 r_free = 0.3261 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 41136 Z= 0.285 Angle : 0.636 5.755 55692 Z= 0.340 Chirality : 0.048 0.240 6300 Planarity : 0.006 0.061 7092 Dihedral : 5.582 56.699 5614 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 41.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.24 % Allowed : 28.57 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.12), residues: 5040 helix: 1.76 (0.14), residues: 1692 sheet: -1.07 (0.18), residues: 804 loop : -2.16 (0.11), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 71 TYR 0.022 0.002 TYR L 195 PHE 0.024 0.003 PHE C 183 TRP 0.009 0.002 TRP K 175 HIS 0.006 0.001 HIS C 164 Details of bonding type rmsd covalent geometry : bond 0.00644 (41100) covalent geometry : angle 0.63646 (55692) hydrogen bonds : bond 0.04356 ( 1764) hydrogen bonds : angle 5.14067 ( 5100) metal coordination : bond 0.00960 ( 24) Misc. bond : bond 0.00026 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 230 poor density : 452 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 HIS cc_start: 0.5221 (m90) cc_final: 0.4434 (m90) REVERT: B 441 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: C 56 ASP cc_start: 0.6981 (m-30) cc_final: 0.6381 (t70) REVERT: C 72 MET cc_start: 0.7374 (tmt) cc_final: 0.6763 (mmm) REVERT: C 123 MET cc_start: 0.7400 (mmm) cc_final: 0.7106 (mpm) REVERT: C 277 ASP cc_start: 0.7405 (m-30) cc_final: 0.7103 (t70) REVERT: C 314 MET cc_start: 0.8610 (tmm) cc_final: 0.8284 (ttp) REVERT: C 377 ASN cc_start: 0.5361 (m110) cc_final: 0.5145 (m-40) REVERT: D 275 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6792 (mtp85) REVERT: D 285 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: D 377 ASN cc_start: 0.5135 (m110) cc_final: 0.4668 (m-40) REVERT: D 441 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.6836 (mp10) REVERT: E 123 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5342 (mpm) REVERT: E 292 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6007 (mtm) REVERT: E 314 MET cc_start: 0.8449 (tmm) cc_final: 0.8182 (tmm) REVERT: E 377 ASN cc_start: 0.4911 (m110) cc_final: 0.4709 (m-40) REVERT: E 441 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: F 72 MET cc_start: 0.4725 (mmt) cc_final: 0.4419 (tmt) REVERT: F 123 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.5510 (mpm) REVERT: F 297 TYR cc_start: 0.6274 (m-10) cc_final: 0.6021 (m-80) REVERT: G 53 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8220 (tt0) REVERT: G 89 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.6991 (m-30) REVERT: G 136 HIS cc_start: 0.5440 (m90) cc_final: 0.4580 (m90) REVERT: G 441 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: H 441 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7303 (mp10) REVERT: I 88 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7070 (tm-30) REVERT: I 277 ASP cc_start: 0.7360 (m-30) cc_final: 0.6840 (t70) REVERT: I 297 TYR cc_start: 0.6713 (m-10) cc_final: 0.6161 (m-10) REVERT: J 88 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7045 (tm-30) REVERT: J 136 HIS cc_start: 0.5511 (m90) cc_final: 0.4549 (m90) REVERT: J 441 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.6851 (mp10) REVERT: K 88 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6981 (tm-30) REVERT: K 441 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: K 465 ARG cc_start: 0.7594 (ppp80) cc_final: 0.7283 (ppp80) REVERT: L 88 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6897 (tm-30) REVERT: L 136 HIS cc_start: 0.5281 (m90) cc_final: 0.4584 (m90) outliers start: 230 outliers final: 126 residues processed: 606 average time/residue: 0.4898 time to fit residues: 376.0575 Evaluate side-chains 579 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 439 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 275 ARG Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 292 MET Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 277 ASP Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 345 ILE Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 89 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 280 VAL Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain H residue 262 SER Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 362 LEU Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 48 ILE Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 378 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 252 optimal weight: 20.0000 chunk 482 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 chunk 353 optimal weight: 0.9980 chunk 254 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 423 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 489 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 448 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS F 377 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 265 HIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 HIS ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.206440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139112 restraints weight = 84128.235| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 3.56 r_work: 0.3454 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 41136 Z= 0.125 Angle : 0.481 5.936 55692 Z= 0.257 Chirality : 0.042 0.145 6300 Planarity : 0.004 0.049 7092 Dihedral : 5.033 57.901 5612 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 38.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.87 % Allowed : 30.92 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.12), residues: 5040 helix: 2.20 (0.14), residues: 1740 sheet: -1.04 (0.18), residues: 804 loop : -2.03 (0.11), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 275 TYR 0.012 0.001 TYR L 195 PHE 0.018 0.001 PHE C 183 TRP 0.007 0.001 TRP H 258 HIS 0.004 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00276 (41100) covalent geometry : angle 0.48093 (55692) hydrogen bonds : bond 0.03006 ( 1764) hydrogen bonds : angle 4.56101 ( 5100) metal coordination : bond 0.00339 ( 24) Misc. bond : bond 0.00035 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 460 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 HIS cc_start: 0.5288 (m90) cc_final: 0.4549 (m90) REVERT: B 441 GLN cc_start: 0.7953 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: C 56 ASP cc_start: 0.6934 (m-30) cc_final: 0.6340 (t70) REVERT: C 72 MET cc_start: 0.7322 (tmt) cc_final: 0.6771 (mmm) REVERT: C 377 ASN cc_start: 0.5501 (m110) cc_final: 0.5287 (m-40) REVERT: C 441 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7401 (mp10) REVERT: D 285 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7661 (m-80) REVERT: D 377 ASN cc_start: 0.5258 (m110) cc_final: 0.4953 (m-40) REVERT: D 441 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.6816 (mp10) REVERT: E 123 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5462 (mpm) REVERT: E 441 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7271 (mp10) REVERT: F 72 MET cc_start: 0.4977 (mmt) cc_final: 0.4580 (tmt) REVERT: F 123 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.5676 (mpm) REVERT: F 297 TYR cc_start: 0.6240 (m-10) cc_final: 0.5970 (m-80) REVERT: F 441 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: G 53 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: G 136 HIS cc_start: 0.5447 (m90) cc_final: 0.4578 (m90) REVERT: G 441 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.6754 (mp10) REVERT: H 88 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6966 (tm-30) REVERT: H 441 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7302 (mp10) REVERT: I 88 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6885 (tm-30) REVERT: I 277 ASP cc_start: 0.7137 (m-30) cc_final: 0.6604 (t70) REVERT: I 297 TYR cc_start: 0.6630 (m-10) cc_final: 0.6180 (m-10) REVERT: I 441 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7690 (mp10) REVERT: J 88 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6936 (tm-30) REVERT: J 136 HIS cc_start: 0.5460 (m90) cc_final: 0.4565 (m90) REVERT: J 441 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.6783 (mp10) REVERT: K 88 GLU cc_start: 0.7397 (tm-30) cc_final: 0.6965 (tm-30) REVERT: K 441 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: K 465 ARG cc_start: 0.7598 (ppp80) cc_final: 0.7287 (ppp80) REVERT: L 88 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6727 (tm-30) REVERT: L 136 HIS cc_start: 0.5301 (m90) cc_final: 0.4638 (m90) REVERT: L 441 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7378 (mp10) outliers start: 126 outliers final: 75 residues processed: 553 average time/residue: 0.4973 time to fit residues: 347.2332 Evaluate side-chains 539 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 449 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 188 MET Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 274 CYS Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 289 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 473 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 417 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 352 optimal weight: 10.0000 chunk 445 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 265 HIS ** H 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 265 HIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 265 HIS ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS K 426 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.203790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.135630 restraints weight = 76481.360| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.59 r_work: 0.3430 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 41136 Z= 0.241 Angle : 0.581 6.143 55692 Z= 0.309 Chirality : 0.046 0.209 6300 Planarity : 0.005 0.057 7092 Dihedral : 5.402 59.246 5612 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 40.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.17 % Allowed : 29.53 % Favored : 66.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.12), residues: 5040 helix: 1.91 (0.14), residues: 1740 sheet: -0.94 (0.18), residues: 780 loop : -2.22 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 275 TYR 0.020 0.002 TYR L 195 PHE 0.022 0.002 PHE C 183 TRP 0.008 0.002 TRP L 175 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00541 (41100) covalent geometry : angle 0.58098 (55692) hydrogen bonds : bond 0.03858 ( 1764) hydrogen bonds : angle 4.91419 ( 5100) metal coordination : bond 0.00816 ( 24) Misc. bond : bond 0.00023 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 453 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 HIS cc_start: 0.5385 (m90) cc_final: 0.4602 (m90) REVERT: B 441 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7259 (mp10) REVERT: C 56 ASP cc_start: 0.6977 (OUTLIER) cc_final: 0.6429 (t70) REVERT: C 72 MET cc_start: 0.7365 (tmt) cc_final: 0.6771 (mmm) REVERT: C 441 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: D 136 HIS cc_start: 0.5287 (m90) cc_final: 0.4499 (m90) REVERT: D 275 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6791 (mtp85) REVERT: D 285 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: D 377 ASN cc_start: 0.5096 (m110) cc_final: 0.4819 (m-40) REVERT: D 441 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.6833 (mp10) REVERT: E 123 MET cc_start: 0.6147 (OUTLIER) cc_final: 0.5471 (mpm) REVERT: E 216 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.7091 (m-30) REVERT: E 441 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: F 123 MET cc_start: 0.6423 (OUTLIER) cc_final: 0.5784 (mpm) REVERT: F 441 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7344 (mp10) REVERT: G 53 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: G 72 MET cc_start: 0.6044 (tpt) cc_final: 0.5509 (tmt) REVERT: G 136 HIS cc_start: 0.5600 (m90) cc_final: 0.4752 (m90) REVERT: G 441 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.6809 (mp10) REVERT: H 88 GLU cc_start: 0.7316 (tm-30) cc_final: 0.7063 (tm-30) REVERT: H 441 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: I 88 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7034 (tm-30) REVERT: I 275 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6861 (mtp85) REVERT: I 277 ASP cc_start: 0.7117 (m-30) cc_final: 0.6656 (t70) REVERT: I 297 TYR cc_start: 0.6702 (m-10) cc_final: 0.6219 (m-10) REVERT: I 441 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7601 (mp10) REVERT: J 53 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: J 88 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7142 (tm-30) REVERT: J 136 HIS cc_start: 0.5552 (m90) cc_final: 0.4683 (m90) REVERT: J 441 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.6796 (mp10) REVERT: K 53 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: K 88 GLU cc_start: 0.7443 (tm-30) cc_final: 0.6991 (tm-30) REVERT: K 441 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: L 88 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6889 (tm-30) REVERT: L 136 HIS cc_start: 0.5494 (m90) cc_final: 0.4846 (m90) REVERT: L 277 ASP cc_start: 0.7056 (m-30) cc_final: 0.6630 (t70) REVERT: L 441 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7327 (mp10) outliers start: 183 outliers final: 117 residues processed: 578 average time/residue: 0.4618 time to fit residues: 340.8003 Evaluate side-chains 577 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 439 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 379 MET Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 275 ARG Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 281 SER Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 53 GLN Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 274 CYS Chi-restraints excluded: chain I residue 275 ARG Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 362 LEU Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 53 GLN Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 138 optimal weight: 9.9990 chunk 402 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 363 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 243 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 347 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 453 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS C 31 GLN ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 GLN C 265 HIS C 377 ASN ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 265 HIS H 429 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 265 HIS ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS K 426 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.204624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.139786 restraints weight = 65818.362| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 3.06 r_work: 0.3497 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 41136 Z= 0.188 Angle : 0.530 6.233 55692 Z= 0.282 Chirality : 0.044 0.169 6300 Planarity : 0.005 0.054 7092 Dihedral : 5.235 59.284 5612 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 39.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 4.01 % Allowed : 29.90 % Favored : 66.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.12), residues: 5040 helix: 2.03 (0.14), residues: 1740 sheet: -1.11 (0.18), residues: 804 loop : -2.11 (0.11), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 275 TYR 0.015 0.002 TYR C 195 PHE 0.021 0.002 PHE D 183 TRP 0.007 0.002 TRP L 175 HIS 0.003 0.001 HIS A 308 Details of bonding type rmsd covalent geometry : bond 0.00421 (41100) covalent geometry : angle 0.53000 (55692) hydrogen bonds : bond 0.03390 ( 1764) hydrogen bonds : angle 4.72814 ( 5100) metal coordination : bond 0.00651 ( 24) Misc. bond : bond 0.00028 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 443 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 HIS cc_start: 0.5451 (m90) cc_final: 0.4703 (m90) REVERT: A 285 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7663 (m-80) REVERT: B 144 ARG cc_start: 0.5666 (OUTLIER) cc_final: 0.5446 (ptm-80) REVERT: B 441 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7337 (mp10) REVERT: C 56 ASP cc_start: 0.7013 (OUTLIER) cc_final: 0.6433 (t70) REVERT: C 72 MET cc_start: 0.7332 (tmt) cc_final: 0.6779 (mmm) REVERT: C 441 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: D 136 HIS cc_start: 0.5350 (m90) cc_final: 0.4580 (m90) REVERT: D 285 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7664 (m-80) REVERT: D 377 ASN cc_start: 0.5213 (m110) cc_final: 0.4933 (m-40) REVERT: D 441 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.6932 (mp10) REVERT: E 123 MET cc_start: 0.6210 (OUTLIER) cc_final: 0.5472 (mpm) REVERT: E 285 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: E 441 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: E 467 ARG cc_start: 0.5162 (mtm-85) cc_final: 0.4827 (mtm-85) REVERT: F 123 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.5789 (mpm) REVERT: F 441 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: G 72 MET cc_start: 0.5950 (tpt) cc_final: 0.5458 (tmt) REVERT: G 136 HIS cc_start: 0.5630 (m90) cc_final: 0.4779 (m90) REVERT: G 285 TYR cc_start: 0.7890 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: G 441 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: H 88 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7003 (tm-30) REVERT: H 216 ASP cc_start: 0.7329 (OUTLIER) cc_final: 0.7064 (m-30) REVERT: H 292 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6203 (mtm) REVERT: H 441 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: I 88 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7040 (tm-30) REVERT: I 277 ASP cc_start: 0.7106 (m-30) cc_final: 0.6651 (t70) REVERT: I 297 TYR cc_start: 0.6629 (m-10) cc_final: 0.6215 (m-10) REVERT: I 441 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: J 88 GLU cc_start: 0.7414 (tm-30) cc_final: 0.7161 (tm-30) REVERT: J 136 HIS cc_start: 0.5593 (m90) cc_final: 0.4801 (m90) REVERT: J 285 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: J 441 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.6844 (mp10) REVERT: K 53 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8353 (tt0) REVERT: K 72 MET cc_start: 0.7139 (tmt) cc_final: 0.6795 (mmt) REVERT: K 88 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7051 (tm-30) REVERT: K 285 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7646 (m-80) REVERT: K 441 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: L 88 GLU cc_start: 0.7278 (tm-30) cc_final: 0.6899 (tm-30) REVERT: L 136 HIS cc_start: 0.5563 (m90) cc_final: 0.4974 (m90) REVERT: L 277 ASP cc_start: 0.6998 (m-30) cc_final: 0.6599 (t70) REVERT: L 441 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7444 (mp10) outliers start: 176 outliers final: 121 residues processed: 571 average time/residue: 0.4772 time to fit residues: 348.0551 Evaluate side-chains 579 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 434 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 56 ASP Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 146 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 242 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 362 LEU Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 146 ASP Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 376 THR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 99 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 147 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 218 THR Chi-restraints excluded: chain E residue 242 SER Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 402 MET Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 147 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 262 SER Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 362 LEU Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 218 THR Chi-restraints excluded: chain H residue 262 SER Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 292 MET Chi-restraints excluded: chain H residue 362 LEU Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 218 THR Chi-restraints excluded: chain I residue 262 SER Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 262 SER Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 53 GLN Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 362 LEU Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 146 ASP Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 181 THR Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 262 SER Chi-restraints excluded: chain L residue 329 SER Chi-restraints excluded: chain L residue 345 ILE Chi-restraints excluded: chain L residue 362 LEU Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 311 optimal weight: 3.9990 chunk 222 optimal weight: 7.9990 chunk 442 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 285 optimal weight: 5.9990 chunk 409 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 358 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 482 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 151 GLN C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 HIS ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 265 HIS ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN J 265 HIS ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS K 426 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.207170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.139181 restraints weight = 76599.047| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.29 r_work: 0.3516 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3494 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 41136 Z= 0.100 Angle : 0.458 6.703 55692 Z= 0.241 Chirality : 0.041 0.124 6300 Planarity : 0.004 0.049 7092 Dihedral : 4.728 56.798 5612 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 37.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.82 % Allowed : 30.92 % Favored : 66.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.13), residues: 5040 helix: 2.40 (0.14), residues: 1740 sheet: -0.92 (0.18), residues: 792 loop : -1.97 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 275 TYR 0.008 0.001 TYR D 150 PHE 0.017 0.001 PHE D 183 TRP 0.008 0.001 TRP E 258 HIS 0.004 0.001 HIS G 308 Details of bonding type rmsd covalent geometry : bond 0.00224 (41100) covalent geometry : angle 0.45790 (55692) hydrogen bonds : bond 0.02620 ( 1764) hydrogen bonds : angle 4.33292 ( 5100) metal coordination : bond 0.00271 ( 24) Misc. bond : bond 0.00036 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 455 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7227 (tm-30) cc_final: 0.7001 (tm-30) REVERT: A 136 HIS cc_start: 0.5325 (m90) cc_final: 0.4631 (m90) REVERT: A 322 ASP cc_start: 0.7113 (m-30) cc_final: 0.6892 (m-30) REVERT: B 24 MET cc_start: 0.7627 (pmm) cc_final: 0.7423 (pmm) REVERT: B 144 ARG cc_start: 0.5573 (OUTLIER) cc_final: 0.5367 (ptm-80) REVERT: B 441 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7424 (mp10) REVERT: C 56 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6405 (t70) REVERT: C 72 MET cc_start: 0.7288 (tmt) cc_final: 0.6811 (mmm) REVERT: C 441 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: D 285 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: D 377 ASN cc_start: 0.5210 (m110) cc_final: 0.4826 (m-40) REVERT: D 441 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.6864 (mp10) REVERT: E 285 TYR cc_start: 0.7835 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: E 441 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: F 72 MET cc_start: 0.4680 (mmt) cc_final: 0.4309 (mpm) REVERT: F 88 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6801 (tm-30) REVERT: F 441 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: G 56 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.6390 (m-30) REVERT: G 72 MET cc_start: 0.6001 (tpt) cc_final: 0.5456 (tmt) REVERT: G 88 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6836 (tm-30) REVERT: G 136 HIS cc_start: 0.5497 (m90) cc_final: 0.4682 (m90) REVERT: G 285 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7637 (m-80) REVERT: G 441 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.6830 (mp10) REVERT: H 88 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6913 (tm-30) REVERT: H 441 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7438 (mp10) REVERT: I 88 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6972 (tm-30) REVERT: I 277 ASP cc_start: 0.7071 (m-30) cc_final: 0.6593 (t70) REVERT: I 297 TYR cc_start: 0.6551 (m-10) cc_final: 0.6341 (m-10) REVERT: I 441 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7696 (mp10) REVERT: J 88 GLU cc_start: 0.7339 (tm-30) cc_final: 0.7041 (tm-30) REVERT: J 136 HIS cc_start: 0.5520 (m90) cc_final: 0.4794 (m90) REVERT: J 441 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.6831 (mp10) REVERT: K 72 MET cc_start: 0.7174 (tmt) cc_final: 0.6817 (mmp) REVERT: K 88 GLU cc_start: 0.7418 (tm-30) cc_final: 0.6987 (tm-30) REVERT: K 285 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.7570 (m-80) REVERT: K 441 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7441 (mp10) REVERT: L 88 GLU cc_start: 0.7245 (tm-30) cc_final: 0.6829 (tm-30) REVERT: L 277 ASP cc_start: 0.6948 (m-30) cc_final: 0.6544 (t70) REVERT: L 441 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7493 (mp10) outliers start: 124 outliers final: 80 residues processed: 546 average time/residue: 0.5038 time to fit residues: 349.0176 Evaluate side-chains 540 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 442 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 147 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 262 SER Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 144 ARG Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 280 VAL Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain E residue 440 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 188 MET Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 6 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 89 ASP Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 411 ARG Chi-restraints excluded: chain I residue 441 GLN Chi-restraints excluded: chain J residue 6 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 218 THR Chi-restraints excluded: chain J residue 274 CYS Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 6 VAL Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 89 ASP Chi-restraints excluded: chain L residue 147 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 216 ASP Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 378 THR Chi-restraints excluded: chain L residue 401 ASP Chi-restraints excluded: chain L residue 441 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 32 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 389 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 248 optimal weight: 0.6980 chunk 270 optimal weight: 2.9990 chunk 500 optimal weight: 0.2980 chunk 205 optimal weight: 0.0270 chunk 189 optimal weight: 0.8980 chunk 245 optimal weight: 0.0770 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 151 GLN C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS D 377 ASN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS F 31 GLN ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN F 265 HIS F 377 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 209 ASN I 265 HIS ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS K 426 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS L 377 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.209196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.143951 restraints weight = 81763.630| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 3.45 r_work: 0.3566 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 41136 Z= 0.080 Angle : 0.436 6.984 55692 Z= 0.226 Chirality : 0.040 0.122 6300 Planarity : 0.004 0.045 7092 Dihedral : 4.234 56.120 5610 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 37.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.00 % Allowed : 31.79 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.13), residues: 5040 helix: 2.66 (0.14), residues: 1740 sheet: -0.49 (0.18), residues: 912 loop : -1.66 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 325 TYR 0.007 0.001 TYR K 382 PHE 0.012 0.001 PHE C 183 TRP 0.006 0.001 TRP A 258 HIS 0.004 0.001 HIS G 308 Details of bonding type rmsd covalent geometry : bond 0.00178 (41100) covalent geometry : angle 0.43586 (55692) hydrogen bonds : bond 0.02317 ( 1764) hydrogen bonds : angle 4.04849 ( 5100) metal coordination : bond 0.00138 ( 24) Misc. bond : bond 0.00034 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 471 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6926 (tm-30) REVERT: A 136 HIS cc_start: 0.5175 (m90) cc_final: 0.4558 (m90) REVERT: A 285 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7526 (m-80) REVERT: B 24 MET cc_start: 0.7544 (pmm) cc_final: 0.7340 (pmm) REVERT: B 441 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7366 (mp10) REVERT: C 56 ASP cc_start: 0.6852 (OUTLIER) cc_final: 0.6385 (t70) REVERT: C 72 MET cc_start: 0.7252 (tmt) cc_final: 0.6807 (mmm) REVERT: C 88 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6874 (tm-30) REVERT: D 136 HIS cc_start: 0.5190 (m90) cc_final: 0.4504 (m90) REVERT: D 285 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: D 441 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6894 (mp10) REVERT: E 285 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: E 467 ARG cc_start: 0.5093 (mtp180) cc_final: 0.4849 (mtm-85) REVERT: F 88 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6788 (tm-30) REVERT: F 411 ARG cc_start: 0.5032 (pmm-80) cc_final: 0.4581 (mtt-85) REVERT: G 56 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.6287 (m-30) REVERT: G 72 MET cc_start: 0.6007 (tpt) cc_final: 0.5498 (tmt) REVERT: G 88 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6909 (tm-30) REVERT: G 427 LYS cc_start: 0.6981 (mtpm) cc_final: 0.6564 (ttmt) REVERT: G 441 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.6820 (mp10) REVERT: H 88 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6817 (tm-30) REVERT: H 441 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: I 277 ASP cc_start: 0.6977 (m-30) cc_final: 0.6493 (t70) REVERT: J 88 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6858 (tm-30) REVERT: J 136 HIS cc_start: 0.5503 (m90) cc_final: 0.4811 (m90) REVERT: J 441 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.6788 (mp10) REVERT: K 72 MET cc_start: 0.7172 (tmt) cc_final: 0.6865 (mmt) REVERT: K 88 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6920 (tm-30) REVERT: K 285 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7529 (m-80) REVERT: K 441 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7442 (mp10) REVERT: L 56 ASP cc_start: 0.7018 (m-30) cc_final: 0.6703 (p0) REVERT: L 72 MET cc_start: 0.7286 (tmt) cc_final: 0.6638 (mmt) REVERT: L 88 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6834 (tm-30) REVERT: L 277 ASP cc_start: 0.6843 (m-30) cc_final: 0.6426 (t70) outliers start: 88 outliers final: 53 residues processed: 533 average time/residue: 0.5089 time to fit residues: 343.6758 Evaluate side-chains 514 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 449 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 337 THR Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 188 MET Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 218 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 170 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 478 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 393 optimal weight: 6.9990 chunk 463 optimal weight: 3.9990 chunk 483 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 265 HIS ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS K 426 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.208394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141226 restraints weight = 83474.770| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.31 r_work: 0.3535 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 41136 Z= 0.187 Angle : 0.564 59.200 55692 Z= 0.318 Chirality : 0.042 0.210 6300 Planarity : 0.004 0.046 7092 Dihedral : 4.250 56.341 5610 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 38.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.71 % Allowed : 32.29 % Favored : 66.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.13), residues: 5040 helix: 2.62 (0.14), residues: 1740 sheet: -0.46 (0.18), residues: 912 loop : -1.64 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 325 TYR 0.028 0.001 TYR I 297 PHE 0.012 0.001 PHE D 183 TRP 0.008 0.002 TRP F 199 HIS 0.003 0.000 HIS K 429 Details of bonding type rmsd covalent geometry : bond 0.00421 (41100) covalent geometry : angle 0.56395 (55692) hydrogen bonds : bond 0.02475 ( 1764) hydrogen bonds : angle 4.06653 ( 5100) metal coordination : bond 0.00725 ( 24) Misc. bond : bond 0.00068 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10080 Ramachandran restraints generated. 5040 Oldfield, 0 Emsley, 5040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 450 time to evaluate : 1.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.7215 (tm-30) cc_final: 0.7006 (tm-30) REVERT: A 136 HIS cc_start: 0.5182 (m90) cc_final: 0.4560 (m90) REVERT: A 285 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: B 441 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7408 (mp10) REVERT: C 56 ASP cc_start: 0.6866 (OUTLIER) cc_final: 0.6385 (t70) REVERT: C 72 MET cc_start: 0.7244 (tmt) cc_final: 0.6809 (mmm) REVERT: C 88 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6877 (tm-30) REVERT: D 136 HIS cc_start: 0.5196 (m90) cc_final: 0.4509 (m90) REVERT: D 285 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: D 441 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.6898 (mp10) REVERT: E 285 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: E 467 ARG cc_start: 0.5080 (mtp180) cc_final: 0.4833 (mtm-85) REVERT: F 88 GLU cc_start: 0.7243 (tm-30) cc_final: 0.6774 (tm-30) REVERT: F 411 ARG cc_start: 0.5019 (pmm-80) cc_final: 0.4552 (mtt-85) REVERT: G 56 ASP cc_start: 0.6509 (OUTLIER) cc_final: 0.6286 (m-30) REVERT: G 72 MET cc_start: 0.6033 (tpt) cc_final: 0.5509 (tmt) REVERT: G 88 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6930 (tm-30) REVERT: G 427 LYS cc_start: 0.7015 (mtpm) cc_final: 0.6587 (ttmt) REVERT: G 441 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.6855 (mp10) REVERT: H 88 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6938 (tm-30) REVERT: H 441 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: I 277 ASP cc_start: 0.7034 (m-30) cc_final: 0.6558 (t70) REVERT: J 88 GLU cc_start: 0.7313 (tm-30) cc_final: 0.6937 (tm-30) REVERT: J 136 HIS cc_start: 0.5519 (m90) cc_final: 0.4826 (m90) REVERT: J 441 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6829 (mp10) REVERT: K 72 MET cc_start: 0.7166 (tmt) cc_final: 0.6884 (mmt) REVERT: K 88 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6928 (tm-30) REVERT: K 285 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7516 (m-80) REVERT: K 441 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: L 56 ASP cc_start: 0.7046 (m-30) cc_final: 0.6697 (p0) REVERT: L 72 MET cc_start: 0.7276 (tmt) cc_final: 0.6634 (mmt) REVERT: L 88 GLU cc_start: 0.7229 (tm-30) cc_final: 0.6859 (tm-30) REVERT: L 277 ASP cc_start: 0.6892 (m-30) cc_final: 0.6552 (t70) outliers start: 75 outliers final: 58 residues processed: 507 average time/residue: 0.5138 time to fit residues: 330.6774 Evaluate side-chains 516 residues out of total 4416 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 446 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain B residue 6 VAL Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 301 THR Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 262 SER Chi-restraints excluded: chain C residue 301 THR Chi-restraints excluded: chain C residue 378 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 262 SER Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 262 SER Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 376 THR Chi-restraints excluded: chain E residue 431 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 181 THR Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain G residue 56 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 139 VAL Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 280 VAL Chi-restraints excluded: chain H residue 376 THR Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 147 VAL Chi-restraints excluded: chain I residue 149 ILE Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 147 VAL Chi-restraints excluded: chain J residue 149 ILE Chi-restraints excluded: chain J residue 165 GLN Chi-restraints excluded: chain J residue 280 VAL Chi-restraints excluded: chain J residue 431 VAL Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 149 ILE Chi-restraints excluded: chain K residue 218 THR Chi-restraints excluded: chain K residue 262 SER Chi-restraints excluded: chain K residue 280 VAL Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain K residue 431 VAL Chi-restraints excluded: chain K residue 441 GLN Chi-restraints excluded: chain L residue 6 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 218 THR Chi-restraints excluded: chain L residue 329 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 411 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 436 optimal weight: 4.9990 chunk 424 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 444 optimal weight: 2.9990 chunk 329 optimal weight: 0.7980 chunk 463 optimal weight: 3.9990 chunk 498 optimal weight: 0.3980 chunk 201 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 HIS ** B 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 265 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS ** D 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 HIS ** F 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** G 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 HIS ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN ** H 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** I 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 265 HIS ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 265 HIS K 426 GLN ** L 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 265 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.208367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152906 restraints weight = 93486.110| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.92 r_work: 0.3554 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 41136 Z= 0.187 Angle : 0.564 59.200 55692 Z= 0.318 Chirality : 0.042 0.210 6300 Planarity : 0.004 0.046 7092 Dihedral : 4.250 56.341 5610 Min Nonbonded Distance : 1.530 Molprobity Statistics. All-atom Clashscore : 38.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.64 % Allowed : 32.33 % Favored : 66.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.13), residues: 5040 helix: 2.62 (0.14), residues: 1740 sheet: -0.46 (0.18), residues: 912 loop : -1.64 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 325 TYR 0.028 0.001 TYR I 297 PHE 0.012 0.001 PHE D 183 TRP 0.008 0.002 TRP F 199 HIS 0.003 0.000 HIS K 429 Details of bonding type rmsd covalent geometry : bond 0.00421 (41100) covalent geometry : angle 0.56395 (55692) hydrogen bonds : bond 0.02475 ( 1764) hydrogen bonds : angle 4.06653 ( 5100) metal coordination : bond 0.00725 ( 24) Misc. bond : bond 0.00068 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16924.61 seconds wall clock time: 289 minutes 6.34 seconds (17346.34 seconds total)