Starting phenix.real_space_refine on Fri Feb 23 08:08:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/02_2024/6z85_11114_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/02_2024/6z85_11114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/02_2024/6z85_11114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/02_2024/6z85_11114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/02_2024/6z85_11114_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/02_2024/6z85_11114_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 18710 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 10 6.06 5 S 130 5.16 5 C 12010 2.51 5 N 3340 2.21 5 O 3390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "K ARG 11": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 66": "NH1" <-> "NH2" Residue "L ARG 11": "NH1" <-> "NH2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "L ARG 66": "NH1" <-> "NH2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 66": "NH1" <-> "NH2" Residue "N ARG 11": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 66": "NH1" <-> "NH2" Residue "O ARG 11": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 66": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 66": "NH1" <-> "NH2" Residue "Q ARG 11": "NH1" <-> "NH2" Residue "Q ARG 38": "NH1" <-> "NH2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ARG 66": "NH1" <-> "NH2" Residue "R ARG 11": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 54": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 66": "NH1" <-> "NH2" Residue "S ARG 11": "NH1" <-> "NH2" Residue "S ARG 38": "NH1" <-> "NH2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 66": "NH1" <-> "NH2" Residue "T ARG 11": "NH1" <-> "NH2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ARG 63": "NH1" <-> "NH2" Residue "T ARG 66": "NH1" <-> "NH2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 184": "NH1" <-> "NH2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 184": "NH1" <-> "NH2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 184": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18880 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "K" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "L" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "M" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "N" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "O" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "P" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "Q" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "R" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "S" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "T" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 652 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 76} Chain: "C" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "D" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "B" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "E" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "G" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "H" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "I" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "J" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "F" Number of atoms: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1218 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain breaks: 2 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 18 Unusual residues: {' ZN': 1, 'HBI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 141 83.878 54.292 79.608 1.00 0.00 S ATOM 1004 SG CYS A 212 81.552 50.817 77.887 1.00 0.00 S ATOM 8188 SG CYS C 141 26.208 41.370 79.550 1.00 0.00 S ATOM 8742 SG CYS C 212 26.119 45.546 77.816 1.00 0.00 S ATOM 9406 SG CYS D 141 29.592 77.627 79.630 1.00 0.00 S ATOM 9960 SG CYS D 212 33.525 79.050 77.909 1.00 0.00 S ATOM 10624 SG CYS B 141 59.669 26.865 79.526 1.00 0.00 S ATOM 11178 SG CYS B 212 55.655 28.048 77.811 1.00 0.00 S ATOM 11842 SG CYS E 141 65.157 85.801 79.575 1.00 0.00 S ATOM 12396 SG CYS E 212 67.753 82.521 77.855 1.00 0.00 S ATOM 13060 SG CYS G 141 59.605 87.561 60.271 1.00 0.00 S ATOM 13614 SG CYS G 212 55.566 86.443 61.969 1.00 0.00 S ATOM 14278 SG CYS H 141 25.929 72.918 60.356 1.00 0.00 S ATOM 14832 SG CYS H 212 25.782 68.742 62.086 1.00 0.00 S ATOM 15496 SG CYS I 141 29.546 36.461 60.443 1.00 0.00 S ATOM 16050 SG CYS I 212 33.479 35.033 62.158 1.00 0.00 S ATOM 16714 SG CYS J 141 65.100 28.652 60.319 1.00 0.00 S ATOM 17268 SG CYS J 212 67.679 31.955 62.019 1.00 0.00 S ATOM 17932 SG CYS F 141 83.848 60.158 60.310 1.00 0.00 S ATOM 18486 SG CYS F 212 81.516 63.626 62.038 1.00 0.00 S Time building chain proxies: 12.49, per 1000 atoms: 0.66 Number of scatterers: 18880 At special positions: 0 Unit cell: (110.931, 115.239, 141.087, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 10 29.99 S 130 16.00 O 3390 8.00 N 3340 7.00 C 12010 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.44 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 141 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 212 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 144 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 141 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 212 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 144 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 141 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 212 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 144 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 141 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 212 " pdb="ZN ZN D 301 " - pdb=" ND1 HIS D 144 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 141 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 212 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 144 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 141 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 212 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 144 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 141 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 212 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 144 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 141 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 212 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 144 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 141 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 212 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 144 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 141 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 212 " pdb="ZN ZN J 301 " - pdb=" ND1 HIS J 144 " 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 40 sheets defined 35.6% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'A' and resid 68 through 81 removed outlier: 3.523A pdb=" N ALA A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.589A pdb=" N PHE A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.526A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 236 removed outlier: 4.037A pdb=" N GLU A 236 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'K' and resid 26 through 32 Processing helix chain 'K' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG K 62 " --> pdb=" O ASP K 58 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 32 Processing helix chain 'L' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG L 62 " --> pdb=" O ASP L 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 32 Processing helix chain 'M' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 32 Processing helix chain 'N' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG N 62 " --> pdb=" O ASP N 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 32 Processing helix chain 'O' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG O 62 " --> pdb=" O ASP O 58 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 32 Processing helix chain 'P' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG P 62 " --> pdb=" O ASP P 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 32 Processing helix chain 'Q' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG Q 62 " --> pdb=" O ASP Q 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 32 Processing helix chain 'R' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG R 62 " --> pdb=" O ASP R 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 32 Processing helix chain 'S' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG S 62 " --> pdb=" O ASP S 58 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 32 Processing helix chain 'T' and resid 53 through 62 removed outlier: 3.689A pdb=" N ARG T 62 " --> pdb=" O ASP T 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 81 removed outlier: 3.523A pdb=" N ALA C 74 " --> pdb=" O ASN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.589A pdb=" N PHE C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.526A pdb=" N LYS C 187 " --> pdb=" O GLU C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 4.036A pdb=" N GLU C 236 " --> pdb=" O VAL C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'D' and resid 68 through 81 removed outlier: 3.524A pdb=" N ALA D 74 " --> pdb=" O ASN D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 removed outlier: 3.589A pdb=" N PHE D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 176 Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.526A pdb=" N LYS D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 236 removed outlier: 4.036A pdb=" N GLU D 236 " --> pdb=" O VAL D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 247 Processing helix chain 'B' and resid 68 through 81 removed outlier: 3.523A pdb=" N ALA B 74 " --> pdb=" O ASN B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 removed outlier: 3.589A pdb=" N PHE B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 176 Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.525A pdb=" N LYS B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 236 removed outlier: 4.036A pdb=" N GLU B 236 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'E' and resid 68 through 81 removed outlier: 3.523A pdb=" N ALA E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 105 removed outlier: 3.590A pdb=" N PHE E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 176 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.526A pdb=" N LYS E 187 " --> pdb=" O GLU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 236 removed outlier: 4.036A pdb=" N GLU E 236 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'G' and resid 68 through 81 removed outlier: 3.524A pdb=" N ALA G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 105 removed outlier: 3.590A pdb=" N PHE G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 176 Processing helix chain 'G' and resid 182 through 197 removed outlier: 3.526A pdb=" N LYS G 187 " --> pdb=" O GLU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 236 removed outlier: 4.036A pdb=" N GLU G 236 " --> pdb=" O VAL G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 247 Processing helix chain 'H' and resid 68 through 81 removed outlier: 3.523A pdb=" N ALA H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 105 removed outlier: 3.589A pdb=" N PHE H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 176 Processing helix chain 'H' and resid 182 through 197 removed outlier: 3.526A pdb=" N LYS H 187 " --> pdb=" O GLU H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 236 removed outlier: 4.036A pdb=" N GLU H 236 " --> pdb=" O VAL H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 247 Processing helix chain 'I' and resid 68 through 81 removed outlier: 3.524A pdb=" N ALA I 74 " --> pdb=" O ASN I 70 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 105 removed outlier: 3.590A pdb=" N PHE I 104 " --> pdb=" O SER I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 176 Processing helix chain 'I' and resid 182 through 197 removed outlier: 3.526A pdb=" N LYS I 187 " --> pdb=" O GLU I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 232 through 236 removed outlier: 4.037A pdb=" N GLU I 236 " --> pdb=" O VAL I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 247 Processing helix chain 'J' and resid 68 through 81 removed outlier: 3.523A pdb=" N ALA J 74 " --> pdb=" O ASN J 70 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 105 removed outlier: 3.590A pdb=" N PHE J 104 " --> pdb=" O SER J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 176 Processing helix chain 'J' and resid 182 through 197 removed outlier: 3.526A pdb=" N LYS J 187 " --> pdb=" O GLU J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 236 removed outlier: 4.036A pdb=" N GLU J 236 " --> pdb=" O VAL J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 247 Processing helix chain 'F' and resid 68 through 81 removed outlier: 3.524A pdb=" N ALA F 74 " --> pdb=" O ASN F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 105 removed outlier: 3.590A pdb=" N PHE F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 176 Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.525A pdb=" N LYS F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 236 removed outlier: 4.036A pdb=" N GLU F 236 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 247 Processing sheet with id= A, first strand: chain 'A' and resid 129 through 132 removed outlier: 3.891A pdb=" N GLY A 201 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 135 through 140 Processing sheet with id= C, first strand: chain 'K' and resid 4 through 8 removed outlier: 3.603A pdb=" N SER K 69 " --> pdb=" O CYS K 80 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'K' and resid 35 through 37 removed outlier: 4.026A pdb=" N GLY K 20 " --> pdb=" O TYR K 47 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL K 49 " --> pdb=" O MET K 18 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N MET K 18 " --> pdb=" O VAL K 49 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 4 through 8 removed outlier: 3.604A pdb=" N SER L 69 " --> pdb=" O CYS L 80 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'L' and resid 35 through 37 removed outlier: 4.026A pdb=" N GLY L 20 " --> pdb=" O TYR L 47 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL L 49 " --> pdb=" O MET L 18 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N MET L 18 " --> pdb=" O VAL L 49 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 4 through 8 removed outlier: 3.604A pdb=" N SER M 69 " --> pdb=" O CYS M 80 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'M' and resid 35 through 37 removed outlier: 4.026A pdb=" N GLY M 20 " --> pdb=" O TYR M 47 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL M 49 " --> pdb=" O MET M 18 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N MET M 18 " --> pdb=" O VAL M 49 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 4 through 8 removed outlier: 3.604A pdb=" N SER N 69 " --> pdb=" O CYS N 80 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 35 through 37 removed outlier: 4.027A pdb=" N GLY N 20 " --> pdb=" O TYR N 47 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL N 49 " --> pdb=" O MET N 18 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N MET N 18 " --> pdb=" O VAL N 49 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'O' and resid 4 through 8 removed outlier: 3.603A pdb=" N SER O 69 " --> pdb=" O CYS O 80 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 35 through 37 removed outlier: 4.026A pdb=" N GLY O 20 " --> pdb=" O TYR O 47 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL O 49 " --> pdb=" O MET O 18 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N MET O 18 " --> pdb=" O VAL O 49 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'P' and resid 4 through 8 removed outlier: 3.603A pdb=" N SER P 69 " --> pdb=" O CYS P 80 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'P' and resid 35 through 37 removed outlier: 4.026A pdb=" N GLY P 20 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL P 49 " --> pdb=" O MET P 18 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N MET P 18 " --> pdb=" O VAL P 49 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Q' and resid 4 through 8 removed outlier: 3.603A pdb=" N SER Q 69 " --> pdb=" O CYS Q 80 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Q' and resid 35 through 37 removed outlier: 4.026A pdb=" N GLY Q 20 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL Q 49 " --> pdb=" O MET Q 18 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N MET Q 18 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'R' and resid 4 through 8 removed outlier: 3.603A pdb=" N SER R 69 " --> pdb=" O CYS R 80 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 35 through 37 removed outlier: 4.026A pdb=" N GLY R 20 " --> pdb=" O TYR R 47 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL R 49 " --> pdb=" O MET R 18 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N MET R 18 " --> pdb=" O VAL R 49 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'S' and resid 4 through 8 removed outlier: 3.604A pdb=" N SER S 69 " --> pdb=" O CYS S 80 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'S' and resid 35 through 37 removed outlier: 4.026A pdb=" N GLY S 20 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL S 49 " --> pdb=" O MET S 18 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N MET S 18 " --> pdb=" O VAL S 49 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'T' and resid 4 through 8 removed outlier: 3.603A pdb=" N SER T 69 " --> pdb=" O CYS T 80 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'T' and resid 35 through 37 removed outlier: 4.026A pdb=" N GLY T 20 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL T 49 " --> pdb=" O MET T 18 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N MET T 18 " --> pdb=" O VAL T 49 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 129 through 132 removed outlier: 3.891A pdb=" N GLY C 201 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 135 through 140 Processing sheet with id= Y, first strand: chain 'D' and resid 129 through 132 removed outlier: 3.891A pdb=" N GLY D 201 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 135 through 140 Processing sheet with id= AA, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.891A pdb=" N GLY B 201 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 135 through 140 Processing sheet with id= AC, first strand: chain 'E' and resid 129 through 132 removed outlier: 3.891A pdb=" N GLY E 201 " --> pdb=" O LEU E 157 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 135 through 140 Processing sheet with id= AE, first strand: chain 'G' and resid 129 through 132 removed outlier: 3.891A pdb=" N GLY G 201 " --> pdb=" O LEU G 157 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 135 through 140 Processing sheet with id= AG, first strand: chain 'H' and resid 129 through 132 removed outlier: 3.890A pdb=" N GLY H 201 " --> pdb=" O LEU H 157 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 135 through 140 Processing sheet with id= AI, first strand: chain 'I' and resid 129 through 132 removed outlier: 3.891A pdb=" N GLY I 201 " --> pdb=" O LEU I 157 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 135 through 140 Processing sheet with id= AK, first strand: chain 'J' and resid 129 through 132 removed outlier: 3.890A pdb=" N GLY J 201 " --> pdb=" O LEU J 157 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 135 through 140 Processing sheet with id= AM, first strand: chain 'F' and resid 129 through 132 removed outlier: 3.892A pdb=" N GLY F 201 " --> pdb=" O LEU F 157 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'F' and resid 135 through 140 910 hydrogen bonds defined for protein. 2520 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.81 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5043 1.33 - 1.45: 3131 1.45 - 1.57: 10816 1.57 - 1.69: 0 1.69 - 1.81: 230 Bond restraints: 19220 Sorted by residual: bond pdb=" C4A HBI D 302 " pdb=" C8A HBI D 302 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.48e+00 bond pdb=" C4A HBI B 302 " pdb=" C8A HBI B 302 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.46e+00 bond pdb=" C4A HBI J 302 " pdb=" C8A HBI J 302 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C4A HBI F 302 " pdb=" C8A HBI F 302 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C4A HBI I 302 " pdb=" C8A HBI I 302 " ideal model delta sigma weight residual 1.397 1.447 -0.050 2.00e-02 2.50e+03 6.35e+00 ... (remaining 19215 not shown) Histogram of bond angle deviations from ideal: 96.69 - 104.14: 360 104.14 - 111.60: 8622 111.60 - 119.05: 6972 119.05 - 126.50: 9776 126.50 - 133.96: 230 Bond angle restraints: 25960 Sorted by residual: angle pdb=" N GLY I 150 " pdb=" CA GLY I 150 " pdb=" C GLY I 150 " ideal model delta sigma weight residual 111.66 118.57 -6.91 1.91e+00 2.74e-01 1.31e+01 angle pdb=" N GLY G 150 " pdb=" CA GLY G 150 " pdb=" C GLY G 150 " ideal model delta sigma weight residual 111.66 118.55 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY H 150 " pdb=" CA GLY H 150 " pdb=" C GLY H 150 " ideal model delta sigma weight residual 111.66 118.55 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY J 150 " pdb=" CA GLY J 150 " pdb=" C GLY J 150 " ideal model delta sigma weight residual 111.66 118.55 -6.89 1.91e+00 2.74e-01 1.30e+01 angle pdb=" N GLY D 150 " pdb=" CA GLY D 150 " pdb=" C GLY D 150 " ideal model delta sigma weight residual 111.66 118.54 -6.88 1.91e+00 2.74e-01 1.30e+01 ... (remaining 25955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 11128 14.52 - 29.03: 482 29.03 - 43.54: 90 43.54 - 58.06: 40 58.06 - 72.57: 10 Dihedral angle restraints: 11750 sinusoidal: 4950 harmonic: 6800 Sorted by residual: dihedral pdb=" CA GLN G 180 " pdb=" C GLN G 180 " pdb=" N VAL G 181 " pdb=" CA VAL G 181 " ideal model delta harmonic sigma weight residual 180.00 148.46 31.54 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA GLN H 180 " pdb=" C GLN H 180 " pdb=" N VAL H 181 " pdb=" CA VAL H 181 " ideal model delta harmonic sigma weight residual 180.00 148.46 31.54 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CA GLN B 180 " pdb=" C GLN B 180 " pdb=" N VAL B 181 " pdb=" CA VAL B 181 " ideal model delta harmonic sigma weight residual 180.00 148.47 31.53 0 5.00e+00 4.00e-02 3.98e+01 ... (remaining 11747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1955 0.053 - 0.106: 762 0.106 - 0.159: 203 0.159 - 0.212: 30 0.212 - 0.265: 20 Chirality restraints: 2970 Sorted by residual: chirality pdb=" CB THR L 17 " pdb=" CA THR L 17 " pdb=" OG1 THR L 17 " pdb=" CG2 THR L 17 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR N 17 " pdb=" CA THR N 17 " pdb=" OG1 THR N 17 " pdb=" CG2 THR N 17 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR O 17 " pdb=" CA THR O 17 " pdb=" OG1 THR O 17 " pdb=" CG2 THR O 17 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2967 not shown) Planarity restraints: 3260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 HBI B 302 " -0.007 2.00e-02 2.50e+03 2.35e-02 1.38e+01 pdb=" C4 HBI B 302 " 0.018 2.00e-02 2.50e+03 pdb=" C4A HBI B 302 " 0.006 2.00e-02 2.50e+03 pdb=" C8A HBI B 302 " -0.006 2.00e-02 2.50e+03 pdb=" N1 HBI B 302 " -0.030 2.00e-02 2.50e+03 pdb=" N2 HBI B 302 " -0.006 2.00e-02 2.50e+03 pdb=" N3 HBI B 302 " 0.017 2.00e-02 2.50e+03 pdb=" N5 HBI B 302 " -0.044 2.00e-02 2.50e+03 pdb=" N8 HBI B 302 " 0.044 2.00e-02 2.50e+03 pdb=" O4 HBI B 302 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 HBI I 302 " -0.007 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" C4 HBI I 302 " 0.018 2.00e-02 2.50e+03 pdb=" C4A HBI I 302 " 0.006 2.00e-02 2.50e+03 pdb=" C8A HBI I 302 " -0.006 2.00e-02 2.50e+03 pdb=" N1 HBI I 302 " -0.029 2.00e-02 2.50e+03 pdb=" N2 HBI I 302 " -0.007 2.00e-02 2.50e+03 pdb=" N3 HBI I 302 " 0.017 2.00e-02 2.50e+03 pdb=" N5 HBI I 302 " -0.044 2.00e-02 2.50e+03 pdb=" N8 HBI I 302 " 0.043 2.00e-02 2.50e+03 pdb=" O4 HBI I 302 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 HBI A 302 " 0.007 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" C4 HBI A 302 " -0.018 2.00e-02 2.50e+03 pdb=" C4A HBI A 302 " -0.006 2.00e-02 2.50e+03 pdb=" C8A HBI A 302 " 0.005 2.00e-02 2.50e+03 pdb=" N1 HBI A 302 " 0.030 2.00e-02 2.50e+03 pdb=" N2 HBI A 302 " 0.006 2.00e-02 2.50e+03 pdb=" N3 HBI A 302 " -0.017 2.00e-02 2.50e+03 pdb=" N5 HBI A 302 " 0.044 2.00e-02 2.50e+03 pdb=" N8 HBI A 302 " -0.043 2.00e-02 2.50e+03 pdb=" O4 HBI A 302 " -0.008 2.00e-02 2.50e+03 ... (remaining 3257 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5385 2.82 - 3.34: 15423 3.34 - 3.86: 30066 3.86 - 4.38: 37977 4.38 - 4.90: 66116 Nonbonded interactions: 154967 Sorted by model distance: nonbonded pdb=" OE1 GLN F 182 " pdb=" OG1 THR F 225 " model vdw 2.301 2.440 nonbonded pdb=" OE1 GLN A 182 " pdb=" OG1 THR A 225 " model vdw 2.301 2.440 nonbonded pdb=" OE1 GLN D 182 " pdb=" OG1 THR D 225 " model vdw 2.301 2.440 nonbonded pdb=" OE1 GLN B 182 " pdb=" OG1 THR B 225 " model vdw 2.301 2.440 nonbonded pdb=" OE1 GLN C 182 " pdb=" OG1 THR C 225 " model vdw 2.301 2.440 ... (remaining 154962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.010 Extract box with map and model: 4.590 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 55.140 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 19220 Z= 0.583 Angle : 1.048 8.904 25960 Z= 0.585 Chirality : 0.062 0.265 2970 Planarity : 0.008 0.052 3260 Dihedral : 9.840 72.575 7350 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.49 % Allowed : 1.46 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.13), residues: 2280 helix: -4.21 (0.08), residues: 880 sheet: -0.71 (0.19), residues: 660 loop : -3.14 (0.16), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP O 79 HIS 0.008 0.002 HIS D 210 PHE 0.043 0.005 PHE F 234 TYR 0.026 0.004 TYR G 75 ARG 0.010 0.001 ARG C 241 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 487 time to evaluate : 2.026 Fit side-chains REVERT: A 242 GLU cc_start: 0.7221 (tt0) cc_final: 0.6657 (tt0) REVERT: C 137 MET cc_start: 0.7250 (tmm) cc_final: 0.7018 (tmm) REVERT: C 143 HIS cc_start: 0.7407 (m170) cc_final: 0.7156 (m-70) REVERT: C 177 ARG cc_start: 0.7695 (mmt180) cc_final: 0.7180 (mpt180) REVERT: D 225 THR cc_start: 0.8356 (p) cc_final: 0.8049 (m) REVERT: B 177 ARG cc_start: 0.7541 (mmt180) cc_final: 0.6915 (mpt180) REVERT: B 194 THR cc_start: 0.8476 (m) cc_final: 0.8207 (m) REVERT: E 168 LEU cc_start: 0.8168 (mt) cc_final: 0.7958 (tp) REVERT: E 225 THR cc_start: 0.7888 (p) cc_final: 0.7635 (m) REVERT: E 242 GLU cc_start: 0.7238 (tt0) cc_final: 0.6829 (OUTLIER) REVERT: G 225 THR cc_start: 0.7981 (p) cc_final: 0.7585 (m) REVERT: H 225 THR cc_start: 0.8131 (p) cc_final: 0.7827 (m) REVERT: H 237 ASP cc_start: 0.7954 (t0) cc_final: 0.7748 (t0) REVERT: I 225 THR cc_start: 0.8425 (p) cc_final: 0.8139 (m) REVERT: J 225 THR cc_start: 0.7938 (p) cc_final: 0.7689 (m) REVERT: F 97 ARG cc_start: 0.7312 (mtt90) cc_final: 0.7091 (mtt90) REVERT: F 225 THR cc_start: 0.8071 (p) cc_final: 0.7553 (m) REVERT: F 242 GLU cc_start: 0.7153 (tt0) cc_final: 0.6694 (mt-10) outliers start: 10 outliers final: 10 residues processed: 497 average time/residue: 1.2151 time to fit residues: 680.2722 Evaluate side-chains 398 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 389 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 73 VAL Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 73 VAL Chi-restraints excluded: chain O residue 73 VAL Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain R residue 73 VAL Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 73 VAL Chi-restraints excluded: chain H residue 189 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 96 optimal weight: 0.0770 chunk 59 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN K 42 ASN L 42 ASN M 42 ASN N 42 ASN O 42 ASN P 42 ASN Q 42 ASN R 42 ASN S 42 ASN T 42 ASN C 180 GLN D 180 GLN D 188 GLN B 143 HIS E 180 GLN H 180 GLN I 180 GLN J 180 GLN F 180 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19220 Z= 0.162 Angle : 0.540 6.012 25960 Z= 0.288 Chirality : 0.044 0.132 2970 Planarity : 0.005 0.044 3260 Dihedral : 6.711 36.919 2720 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.94 % Allowed : 10.83 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.16), residues: 2280 helix: -1.23 (0.16), residues: 890 sheet: -0.09 (0.20), residues: 690 loop : -2.42 (0.18), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 79 HIS 0.010 0.001 HIS N 31 PHE 0.017 0.002 PHE C 148 TYR 0.013 0.001 TYR J 156 ARG 0.003 0.000 ARG I 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 375 time to evaluate : 1.981 Fit side-chains REVERT: A 211 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.5995 (mmm) REVERT: N 18 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.6288 (mmt) REVERT: N 37 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6196 (ptt90) REVERT: O 51 ASP cc_start: 0.6757 (m-30) cc_final: 0.6424 (m-30) REVERT: T 51 ASP cc_start: 0.6787 (m-30) cc_final: 0.6373 (m-30) REVERT: C 137 MET cc_start: 0.7185 (tmm) cc_final: 0.6876 (tmm) REVERT: C 143 HIS cc_start: 0.7650 (m170) cc_final: 0.7439 (m-70) REVERT: C 211 MET cc_start: 0.6428 (mtm) cc_final: 0.5843 (mmm) REVERT: D 134 ASP cc_start: 0.6938 (m-30) cc_final: 0.6625 (m-30) REVERT: D 173 GLU cc_start: 0.6081 (tm-30) cc_final: 0.5403 (tt0) REVERT: B 177 ARG cc_start: 0.7560 (mmt180) cc_final: 0.6869 (mpt180) REVERT: E 178 ARG cc_start: 0.7808 (mtt180) cc_final: 0.7604 (mtt180) REVERT: E 211 MET cc_start: 0.6430 (OUTLIER) cc_final: 0.5866 (mmm) REVERT: G 128 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6282 (pt0) REVERT: G 228 SER cc_start: 0.8490 (m) cc_final: 0.8248 (t) REVERT: H 140 MET cc_start: 0.7854 (mmm) cc_final: 0.7320 (tpp) REVERT: I 79 LEU cc_start: 0.6940 (mt) cc_final: 0.6721 (mm) REVERT: I 134 ASP cc_start: 0.6947 (m-30) cc_final: 0.6647 (m-30) REVERT: I 211 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5658 (mtm) REVERT: J 129 MET cc_start: 0.7735 (ttm) cc_final: 0.7287 (mtt) REVERT: J 178 ARG cc_start: 0.7708 (mtt180) cc_final: 0.7489 (mtt180) REVERT: J 211 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5619 (OUTLIER) REVERT: J 242 GLU cc_start: 0.7364 (tt0) cc_final: 0.7157 (mt-10) REVERT: F 134 ASP cc_start: 0.6928 (m-30) cc_final: 0.6706 (m-30) outliers start: 40 outliers final: 8 residues processed: 390 average time/residue: 1.0467 time to fit residues: 468.3286 Evaluate side-chains 362 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 348 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain N residue 18 MET Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain P residue 73 VAL Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 12 MET Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 211 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 142 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Q 23 GLN C 143 HIS C 180 GLN D 180 GLN E 143 HIS E 180 GLN G 143 HIS H 143 HIS I 180 GLN J 143 HIS F 143 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19220 Z= 0.295 Angle : 0.632 7.521 25960 Z= 0.325 Chirality : 0.047 0.143 2970 Planarity : 0.005 0.039 3260 Dihedral : 6.884 41.229 2712 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.45 % Allowed : 11.70 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2280 helix: 0.12 (0.17), residues: 870 sheet: 1.08 (0.23), residues: 560 loop : -2.11 (0.16), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 96 HIS 0.006 0.001 HIS N 31 PHE 0.021 0.003 PHE H 148 TYR 0.016 0.002 TYR H 156 ARG 0.005 0.001 ARG G 235 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 366 time to evaluate : 2.139 Fit side-chains REVERT: A 183 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6780 (mt-10) REVERT: A 211 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6309 (mmm) REVERT: K 5 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7941 (mt) REVERT: M 5 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8057 (mt) REVERT: N 37 ARG cc_start: 0.6928 (OUTLIER) cc_final: 0.6187 (ptt90) REVERT: O 37 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6749 (ptt180) REVERT: O 51 ASP cc_start: 0.6812 (m-30) cc_final: 0.6453 (m-30) REVERT: T 51 ASP cc_start: 0.6799 (m-30) cc_final: 0.6408 (m-30) REVERT: C 77 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7225 (m) REVERT: C 211 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6485 (mmm) REVERT: D 134 ASP cc_start: 0.6982 (m-30) cc_final: 0.6654 (m-30) REVERT: D 211 MET cc_start: 0.6817 (OUTLIER) cc_final: 0.6417 (mmm) REVERT: B 128 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6534 (pt0) REVERT: E 178 ARG cc_start: 0.7864 (mtt180) cc_final: 0.7646 (mtt180) REVERT: E 211 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6160 (mmm) REVERT: G 128 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6323 (pt0) REVERT: H 140 MET cc_start: 0.7999 (mmm) cc_final: 0.7479 (tpp) REVERT: I 134 ASP cc_start: 0.6972 (m-30) cc_final: 0.6674 (m-30) REVERT: I 183 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6852 (mt-10) REVERT: I 211 MET cc_start: 0.6238 (OUTLIER) cc_final: 0.5756 (mmm) REVERT: J 102 MET cc_start: 0.5988 (tpt) cc_final: 0.5747 (mmt) REVERT: J 211 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.6224 (mmm) REVERT: F 140 MET cc_start: 0.7890 (mmm) cc_final: 0.7655 (tpp) REVERT: F 211 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6134 (mmm) outliers start: 71 outliers final: 20 residues processed: 396 average time/residue: 1.0678 time to fit residues: 486.8403 Evaluate side-chains 373 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 339 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain T residue 12 MET Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 222 optimal weight: 0.3980 chunk 109 optimal weight: 0.6980 chunk 199 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS L 23 GLN Q 23 GLN C 143 HIS D 180 GLN H 143 HIS I 180 GLN J 180 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6722 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19220 Z= 0.197 Angle : 0.543 6.203 25960 Z= 0.280 Chirality : 0.044 0.143 2970 Planarity : 0.004 0.038 3260 Dihedral : 6.127 37.744 2710 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.20 % Allowed : 13.93 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2280 helix: 0.99 (0.18), residues: 870 sheet: 1.23 (0.23), residues: 560 loop : -1.87 (0.17), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 79 HIS 0.010 0.001 HIS L 31 PHE 0.018 0.002 PHE F 148 TYR 0.013 0.002 TYR C 156 ARG 0.003 0.000 ARG G 235 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 352 time to evaluate : 2.085 Fit side-chains REVERT: A 211 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6312 (mmm) REVERT: M 5 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8073 (mt) REVERT: N 37 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6140 (ptt90) REVERT: O 51 ASP cc_start: 0.6725 (m-30) cc_final: 0.6298 (m-30) REVERT: S 12 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6151 (pmt) REVERT: T 51 ASP cc_start: 0.6709 (m-30) cc_final: 0.6316 (m-30) REVERT: C 77 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7243 (m) REVERT: C 211 MET cc_start: 0.6890 (OUTLIER) cc_final: 0.6277 (mmm) REVERT: D 128 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6712 (pp20) REVERT: D 211 MET cc_start: 0.6808 (mtm) cc_final: 0.6405 (mmm) REVERT: E 128 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.6582 (pp20) REVERT: E 211 MET cc_start: 0.6793 (OUTLIER) cc_final: 0.6269 (mmm) REVERT: G 128 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6440 (pt0) REVERT: G 211 MET cc_start: 0.6574 (mtp) cc_final: 0.6371 (mtp) REVERT: H 140 MET cc_start: 0.7861 (mmm) cc_final: 0.7408 (tpp) REVERT: H 211 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6220 (mmm) REVERT: I 134 ASP cc_start: 0.6986 (m-30) cc_final: 0.6682 (m-30) REVERT: I 211 MET cc_start: 0.6177 (OUTLIER) cc_final: 0.5768 (mmm) REVERT: J 168 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7715 (mp) REVERT: J 211 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6124 (mmm) REVERT: F 140 MET cc_start: 0.7802 (mmm) cc_final: 0.7580 (tpp) REVERT: F 211 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6122 (mmm) outliers start: 66 outliers final: 24 residues processed: 382 average time/residue: 0.9972 time to fit residues: 440.8824 Evaluate side-chains 366 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 327 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain T residue 12 MET Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 211 MET Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 199 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 GLN Q 23 GLN C 143 HIS D 180 GLN I 180 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19220 Z= 0.171 Angle : 0.515 5.787 25960 Z= 0.266 Chirality : 0.044 0.142 2970 Planarity : 0.004 0.038 3260 Dihedral : 5.684 35.790 2710 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.35 % Allowed : 13.93 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2280 helix: 1.48 (0.18), residues: 880 sheet: 1.30 (0.23), residues: 560 loop : -1.81 (0.16), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 79 HIS 0.008 0.001 HIS L 31 PHE 0.018 0.002 PHE G 244 TYR 0.013 0.001 TYR C 156 ARG 0.002 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 346 time to evaluate : 2.207 Fit side-chains REVERT: A 211 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6258 (mmm) REVERT: M 5 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8015 (mt) REVERT: N 37 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6103 (ptt90) REVERT: O 12 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6512 (pmt) REVERT: O 51 ASP cc_start: 0.6767 (m-30) cc_final: 0.6369 (m-30) REVERT: P 12 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6561 (pmt) REVERT: R 5 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7897 (mt) REVERT: T 51 ASP cc_start: 0.6748 (m-30) cc_final: 0.6382 (m-30) REVERT: C 77 SER cc_start: 0.7686 (OUTLIER) cc_final: 0.7258 (m) REVERT: C 211 MET cc_start: 0.6863 (OUTLIER) cc_final: 0.6209 (mmm) REVERT: D 211 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6425 (mmm) REVERT: E 128 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6644 (pp20) REVERT: E 129 MET cc_start: 0.7550 (OUTLIER) cc_final: 0.6898 (mmt) REVERT: E 211 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.6268 (mmm) REVERT: G 128 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6466 (pt0) REVERT: G 211 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.6315 (mtp) REVERT: H 140 MET cc_start: 0.7848 (mmm) cc_final: 0.7437 (tpp) REVERT: H 211 MET cc_start: 0.6808 (mtm) cc_final: 0.6168 (mmm) REVERT: I 134 ASP cc_start: 0.6946 (m-30) cc_final: 0.6632 (m-30) REVERT: I 211 MET cc_start: 0.6101 (OUTLIER) cc_final: 0.5689 (mmm) REVERT: J 128 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.6536 (pp20) REVERT: J 168 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7686 (mp) REVERT: J 211 MET cc_start: 0.6903 (OUTLIER) cc_final: 0.6356 (mmm) REVERT: F 211 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6195 (mmm) outliers start: 69 outliers final: 30 residues processed: 377 average time/residue: 1.0423 time to fit residues: 453.9691 Evaluate side-chains 381 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 332 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 51 ASP Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain R residue 5 LEU Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 9.9990 chunk 200 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 73 optimal weight: 0.0050 chunk 116 optimal weight: 7.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 23 GLN Q 23 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19220 Z= 0.192 Angle : 0.533 6.179 25960 Z= 0.273 Chirality : 0.044 0.150 2970 Planarity : 0.004 0.039 3260 Dihedral : 5.639 34.421 2710 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.45 % Allowed : 14.17 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.17), residues: 2280 helix: 1.66 (0.18), residues: 880 sheet: 1.33 (0.23), residues: 560 loop : -1.73 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 79 HIS 0.007 0.001 HIS L 31 PHE 0.024 0.002 PHE G 244 TYR 0.014 0.001 TYR B 109 ARG 0.003 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 349 time to evaluate : 2.131 Fit side-chains REVERT: A 211 MET cc_start: 0.7085 (OUTLIER) cc_final: 0.6233 (mmm) REVERT: M 5 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7983 (mt) REVERT: N 37 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6089 (ptt90) REVERT: O 51 ASP cc_start: 0.6716 (m-30) cc_final: 0.6345 (m-30) REVERT: R 46 GLU cc_start: 0.7448 (pt0) cc_final: 0.7116 (pt0) REVERT: S 12 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6258 (pmt) REVERT: T 51 ASP cc_start: 0.6711 (m-30) cc_final: 0.6357 (m-30) REVERT: C 77 SER cc_start: 0.7704 (OUTLIER) cc_final: 0.7294 (m) REVERT: C 183 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6469 (mt-10) REVERT: C 211 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6172 (mmm) REVERT: D 211 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6561 (mmm) REVERT: D 224 LYS cc_start: 0.7793 (mmmt) cc_final: 0.7564 (mmmt) REVERT: B 211 MET cc_start: 0.7111 (mmm) cc_final: 0.6860 (mmp) REVERT: E 128 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6580 (pp20) REVERT: E 129 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6863 (mmt) REVERT: E 211 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6492 (mmm) REVERT: G 128 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.6509 (pt0) REVERT: G 211 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6279 (mtp) REVERT: H 140 MET cc_start: 0.7842 (mmm) cc_final: 0.7465 (tpp) REVERT: J 128 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.6526 (pp20) REVERT: J 168 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7767 (mp) REVERT: J 211 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6658 (mmm) REVERT: F 211 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6153 (mmm) outliers start: 71 outliers final: 39 residues processed: 387 average time/residue: 1.0354 time to fit residues: 463.3336 Evaluate side-chains 392 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 337 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 37 ARG Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 12 MET Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 211 MET Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 124 optimal weight: 0.3980 chunk 221 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19220 Z= 0.161 Angle : 0.504 5.569 25960 Z= 0.259 Chirality : 0.043 0.146 2970 Planarity : 0.003 0.040 3260 Dihedral : 5.268 30.756 2710 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.16 % Allowed : 14.66 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.18), residues: 2280 helix: 1.94 (0.18), residues: 880 sheet: 1.39 (0.23), residues: 560 loop : -1.58 (0.17), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 79 HIS 0.007 0.001 HIS L 31 PHE 0.022 0.002 PHE G 244 TYR 0.012 0.001 TYR C 156 ARG 0.002 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 350 time to evaluate : 2.533 Fit side-chains REVERT: A 211 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6177 (mmm) REVERT: L 65 PHE cc_start: 0.7609 (m-80) cc_final: 0.7399 (m-10) REVERT: M 5 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7949 (mt) REVERT: O 12 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6658 (pmt) REVERT: O 29 MET cc_start: 0.7375 (mmp) cc_final: 0.6610 (mmp) REVERT: O 51 ASP cc_start: 0.6730 (m-30) cc_final: 0.6352 (m-30) REVERT: R 46 GLU cc_start: 0.7392 (pt0) cc_final: 0.7115 (pt0) REVERT: T 51 ASP cc_start: 0.6683 (m-30) cc_final: 0.6378 (m-30) REVERT: C 77 SER cc_start: 0.7720 (OUTLIER) cc_final: 0.7293 (m) REVERT: C 183 GLU cc_start: 0.6925 (mt-10) cc_final: 0.6455 (mt-10) REVERT: C 211 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6084 (mmm) REVERT: D 211 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6417 (mmm) REVERT: D 224 LYS cc_start: 0.7772 (mmmt) cc_final: 0.7384 (mttt) REVERT: E 129 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7322 (mmt) REVERT: E 211 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6350 (mmm) REVERT: G 128 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6582 (pt0) REVERT: H 140 MET cc_start: 0.7830 (mmm) cc_final: 0.7458 (tpp) REVERT: J 128 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6476 (pp20) REVERT: J 129 MET cc_start: 0.7612 (ttm) cc_final: 0.7020 (mtt) REVERT: J 168 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7732 (mp) REVERT: J 211 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6621 (mmm) REVERT: F 211 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.6138 (mmm) outliers start: 65 outliers final: 39 residues processed: 382 average time/residue: 0.9924 time to fit residues: 440.9835 Evaluate side-chains 383 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 331 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 19 VAL Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 128 GLU Chi-restraints excluded: chain G residue 129 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 chunk 140 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 174 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 23 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 19220 Z= 0.147 Angle : 0.492 5.241 25960 Z= 0.253 Chirality : 0.043 0.144 2970 Planarity : 0.003 0.039 3260 Dihedral : 4.989 28.576 2710 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.91 % Allowed : 15.00 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.18), residues: 2280 helix: 2.15 (0.18), residues: 880 sheet: 0.87 (0.21), residues: 670 loop : -1.60 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 79 HIS 0.006 0.001 HIS L 31 PHE 0.019 0.002 PHE B 244 TYR 0.011 0.001 TYR H 156 ARG 0.002 0.000 ARG J 178 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 346 time to evaluate : 1.993 Fit side-chains REVERT: A 211 MET cc_start: 0.6823 (OUTLIER) cc_final: 0.6175 (mmm) REVERT: K 5 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7756 (mt) REVERT: M 5 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7891 (mt) REVERT: O 12 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6721 (pmt) REVERT: O 29 MET cc_start: 0.7344 (mmp) cc_final: 0.6626 (mmp) REVERT: O 51 ASP cc_start: 0.6644 (m-30) cc_final: 0.6262 (m-30) REVERT: R 46 GLU cc_start: 0.7365 (pt0) cc_final: 0.7122 (pt0) REVERT: T 51 ASP cc_start: 0.6657 (m-30) cc_final: 0.6368 (m-30) REVERT: C 77 SER cc_start: 0.7694 (OUTLIER) cc_final: 0.7286 (m) REVERT: C 183 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6596 (mt-10) REVERT: C 211 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.6147 (mmm) REVERT: D 128 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6723 (pp20) REVERT: D 211 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6400 (mmm) REVERT: D 224 LYS cc_start: 0.7671 (mmmt) cc_final: 0.7288 (mttt) REVERT: E 128 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6630 (pp20) REVERT: E 129 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6924 (mmt) REVERT: E 211 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6259 (mmm) REVERT: H 140 MET cc_start: 0.7724 (mmm) cc_final: 0.7330 (tpp) REVERT: I 183 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6871 (mt-10) REVERT: I 211 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.5511 (mmm) REVERT: J 128 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6535 (pp20) REVERT: J 129 MET cc_start: 0.7568 (ttm) cc_final: 0.6769 (mtt) REVERT: J 168 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7719 (mp) REVERT: J 211 MET cc_start: 0.6945 (OUTLIER) cc_final: 0.6688 (mmm) REVERT: F 211 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6138 (mmm) outliers start: 60 outliers final: 28 residues processed: 376 average time/residue: 1.0128 time to fit residues: 441.7638 Evaluate side-chains 377 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 333 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 246 THR Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 8.9990 chunk 212 optimal weight: 0.8980 chunk 193 optimal weight: 0.0870 chunk 206 optimal weight: 4.9990 chunk 124 optimal weight: 0.0470 chunk 89 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 195 optimal weight: 0.9990 chunk 205 optimal weight: 0.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19220 Z= 0.144 Angle : 0.490 5.990 25960 Z= 0.251 Chirality : 0.043 0.148 2970 Planarity : 0.003 0.039 3260 Dihedral : 4.793 26.205 2710 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.33 % Allowed : 15.53 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.18), residues: 2280 helix: 2.29 (0.18), residues: 880 sheet: 0.95 (0.21), residues: 670 loop : -1.51 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 79 HIS 0.006 0.001 HIS L 31 PHE 0.017 0.002 PHE G 244 TYR 0.010 0.001 TYR E 109 ARG 0.002 0.000 ARG J 178 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 355 time to evaluate : 2.138 Fit side-chains REVERT: A 168 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7907 (mp) REVERT: A 211 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6261 (mmm) REVERT: K 5 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7785 (mt) REVERT: M 5 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7879 (mt) REVERT: O 12 MET cc_start: 0.7011 (OUTLIER) cc_final: 0.6808 (pmt) REVERT: O 29 MET cc_start: 0.7343 (mmp) cc_final: 0.6664 (mmp) REVERT: O 51 ASP cc_start: 0.6623 (m-30) cc_final: 0.6254 (m-30) REVERT: R 46 GLU cc_start: 0.7425 (pt0) cc_final: 0.7149 (pt0) REVERT: T 29 MET cc_start: 0.7262 (mmp) cc_final: 0.6526 (mmp) REVERT: T 51 ASP cc_start: 0.6613 (m-30) cc_final: 0.6257 (m-30) REVERT: C 77 SER cc_start: 0.7672 (OUTLIER) cc_final: 0.7271 (m) REVERT: C 183 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6450 (mt-10) REVERT: C 211 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.6078 (mmm) REVERT: D 211 MET cc_start: 0.6777 (OUTLIER) cc_final: 0.6371 (mmm) REVERT: D 224 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7289 (mttt) REVERT: E 97 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7451 (mtm180) REVERT: E 128 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6625 (pp20) REVERT: E 129 MET cc_start: 0.7461 (OUTLIER) cc_final: 0.6919 (mmt) REVERT: E 168 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7648 (mp) REVERT: E 211 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6073 (mmm) REVERT: H 140 MET cc_start: 0.7671 (mmm) cc_final: 0.7314 (tpp) REVERT: I 183 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6870 (mt-10) REVERT: I 211 MET cc_start: 0.5962 (OUTLIER) cc_final: 0.5502 (mmm) REVERT: J 128 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.6483 (pp20) REVERT: J 129 MET cc_start: 0.7554 (ttm) cc_final: 0.6997 (mtt) REVERT: J 168 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7712 (mp) REVERT: J 211 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6704 (mmm) REVERT: F 211 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.5927 (mmm) outliers start: 48 outliers final: 27 residues processed: 383 average time/residue: 0.9779 time to fit residues: 434.6595 Evaluate side-chains 386 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 342 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 168 LEU Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 133 optimal weight: 0.2980 chunk 103 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 229 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 182 optimal weight: 0.3980 chunk 18 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19220 Z= 0.155 Angle : 0.502 8.095 25960 Z= 0.256 Chirality : 0.043 0.148 2970 Planarity : 0.003 0.039 3260 Dihedral : 4.774 25.555 2710 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.43 % Allowed : 15.24 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 2280 helix: 2.28 (0.18), residues: 880 sheet: 1.00 (0.21), residues: 670 loop : -1.48 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 79 HIS 0.006 0.001 HIS L 31 PHE 0.017 0.002 PHE G 244 TYR 0.011 0.001 TYR J 175 ARG 0.002 0.000 ARG A 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 346 time to evaluate : 2.055 Fit side-chains REVERT: A 211 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6038 (mmm) REVERT: K 5 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7796 (mt) REVERT: M 5 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7878 (mt) REVERT: O 12 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6817 (pmt) REVERT: O 29 MET cc_start: 0.7341 (mmp) cc_final: 0.6699 (mmp) REVERT: O 51 ASP cc_start: 0.6616 (m-30) cc_final: 0.6241 (m-30) REVERT: R 29 MET cc_start: 0.6989 (mmp) cc_final: 0.6593 (mmp) REVERT: R 46 GLU cc_start: 0.7390 (pt0) cc_final: 0.7153 (pt0) REVERT: T 29 MET cc_start: 0.7257 (mmp) cc_final: 0.6543 (mmp) REVERT: T 51 ASP cc_start: 0.6550 (m-30) cc_final: 0.6239 (m-30) REVERT: C 77 SER cc_start: 0.7667 (OUTLIER) cc_final: 0.7274 (m) REVERT: C 183 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6626 (mt-10) REVERT: D 128 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6712 (pp20) REVERT: D 211 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6400 (mmm) REVERT: D 224 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7326 (mttt) REVERT: E 97 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7449 (mtm180) REVERT: E 128 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6608 (pp20) REVERT: E 129 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6940 (mmt) REVERT: E 211 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6122 (mmm) REVERT: G 129 MET cc_start: 0.6951 (mmt) cc_final: 0.6708 (mmt) REVERT: H 140 MET cc_start: 0.7746 (mmm) cc_final: 0.7388 (tpp) REVERT: I 183 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6865 (mt-10) REVERT: I 211 MET cc_start: 0.6011 (OUTLIER) cc_final: 0.5550 (mmm) REVERT: J 128 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6473 (pp20) REVERT: J 129 MET cc_start: 0.7585 (ttm) cc_final: 0.6866 (mtt) REVERT: J 168 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7732 (mp) REVERT: J 211 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6749 (mmm) REVERT: F 211 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.5978 (mmm) REVERT: F 230 MET cc_start: 0.8265 (mmt) cc_final: 0.7861 (mmm) outliers start: 50 outliers final: 29 residues processed: 373 average time/residue: 1.0698 time to fit residues: 464.3071 Evaluate side-chains 382 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 338 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 76 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 76 THR Chi-restraints excluded: chain M residue 5 LEU Chi-restraints excluded: chain M residue 76 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain O residue 12 MET Chi-restraints excluded: chain O residue 76 THR Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain Q residue 76 THR Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain S residue 76 THR Chi-restraints excluded: chain T residue 76 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 129 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain G residue 168 LEU Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain I residue 211 MET Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 211 MET Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 211 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 4.9990 chunk 194 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 76 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.239700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.212630 restraints weight = 15754.345| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 1.30 r_work: 0.4202 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.4096 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 19220 Z= 0.318 Angle : 0.652 12.739 25960 Z= 0.327 Chirality : 0.048 0.158 2970 Planarity : 0.004 0.039 3260 Dihedral : 6.140 36.556 2710 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.86 % Allowed : 15.15 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2280 helix: 1.51 (0.17), residues: 880 sheet: 0.89 (0.21), residues: 670 loop : -1.82 (0.18), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 96 HIS 0.005 0.001 HIS L 31 PHE 0.025 0.003 PHE D 105 TYR 0.024 0.002 TYR J 109 ARG 0.004 0.001 ARG B 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7352.47 seconds wall clock time: 131 minutes 23.86 seconds (7883.86 seconds total)