Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 16:02:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/05_2023/6z85_11114_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/05_2023/6z85_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_11114/05_2023/6z85_11114.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/05_2023/6z85_11114.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/05_2023/6z85_11114_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z85_11114/05_2023/6z85_11114_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 11.31, per 1000 atoms: 0.60 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: 6.55 Conformation dependent library (CDL) restraints added in 2.5 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: 1.42 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: 6.21 Time building geometry restraints manager: 7.10 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: 11098 14.52 - 29.03: 452 29.03 - 43.54: 60 43.54 - 58.06: 30 58.06 - 72.57: 10 Dihedral angle restraints: 11650 sinusoidal: 4850 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 11647 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.420 Construct map_model_manager: 0.020 Extract box with map and model: 4.700 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 54.270 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.830 ------------------------------------------------------------------------------- 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 : 9.336 72.575 7250 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 % 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 *********************** 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 : 2.523 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 497 average time/residue: 1.1898 time to fit residues: 665.9934 Evaluate side-chains 394 residues out of total 2060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 384 time to evaluate : 1.665 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 2 average time/residue: 0.7790 time to fit residues: 4.1104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: