Starting phenix.real_space_refine on Mon Feb 19 18:36:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2024/7phk_13418_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2024/7phk_13418.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2024/7phk_13418_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2024/7phk_13418_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2024/7phk_13418_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2024/7phk_13418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2024/7phk_13418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2024/7phk_13418_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2024/7phk_13418_updated.pdb" } resolution = 3.1 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= 0.006 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 8 8.98 5 Zn 8 6.06 5 P 16 5.49 5 S 136 5.16 5 C 16648 2.51 5 N 4216 2.21 5 O 4372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ARG 9": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ARG 9": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C GLU 116": "OE1" <-> "OE2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 380": "OE1" <-> "OE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ARG 9": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B GLU 116": "OE1" <-> "OE2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 242": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D ARG 9": "NH1" <-> "NH2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D ARG 190": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "D GLU 242": "OE1" <-> "OE2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D GLU 380": "OE1" <-> "OE2" Residue "E GLU 8": "OE1" <-> "OE2" Residue "E ARG 9": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E ARG 190": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E GLU 380": "OE1" <-> "OE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G ARG 9": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ARG 190": "NH1" <-> "NH2" Residue "G ARG 214": "NH1" <-> "NH2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "G GLU 242": "OE1" <-> "OE2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G GLU 380": "OE1" <-> "OE2" Residue "F GLU 8": "OE1" <-> "OE2" Residue "F ARG 9": "NH1" <-> "NH2" Residue "F ARG 51": "NH1" <-> "NH2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F GLU 238": "OE1" <-> "OE2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F ARG 332": "NH1" <-> "NH2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F GLU 380": "OE1" <-> "OE2" Residue "H GLU 8": "OE1" <-> "OE2" Residue "H ARG 9": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H ARG 190": "NH1" <-> "NH2" Residue "H ARG 214": "NH1" <-> "NH2" Residue "H GLU 238": "OE1" <-> "OE2" Residue "H GLU 242": "OE1" <-> "OE2" Residue "H GLU 259": "OE1" <-> "OE2" Residue "H ARG 332": "NH1" <-> "NH2" Residue "H ARG 339": "NH1" <-> "NH2" Residue "H GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25404 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3095 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3095 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3095 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "D" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3095 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 21, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "E" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "G" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "F" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "H" Number of atoms: 3098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3098 Classifications: {'peptide': 393} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4, 'TYR:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "A" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {' K': 4, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "B" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "D" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {' K': 4, ' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "G" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "F" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 78 Unusual residues: {' ZN': 1, 'PCF': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 798 SG CYS A 104 77.866 68.367 155.359 1.00107.92 S ATOM 804 SG CYS A 105 77.166 65.043 154.127 1.00105.62 S ATOM 6819 SG CYS B 83 74.366 66.914 153.257 1.00103.76 S ATOM 3893 SG CYS C 104 49.706 59.250 155.299 1.00107.92 S ATOM 3899 SG CYS C 105 50.414 62.572 154.065 1.00105.62 S ATOM 9914 SG CYS D 83 53.218 60.823 153.289 1.00103.76 S ATOM 3724 SG CYS C 83 60.743 74.324 153.224 1.00103.76 S ATOM 6988 SG CYS B 104 59.224 77.865 155.286 1.00107.92 S ATOM 6994 SG CYS B 105 62.552 77.175 154.059 1.00105.62 S ATOM 629 SG CYS A 83 66.867 53.263 153.309 1.00103.76 S ATOM 10083 SG CYS D 104 68.302 49.795 155.335 1.00107.92 S ATOM 10089 SG CYS D 105 64.978 50.501 154.105 1.00105.62 S ATOM 13178 SG CYS E 104 77.957 68.173 76.846 1.00107.92 S ATOM 13184 SG CYS E 105 75.487 70.505 78.080 1.00105.62 S ATOM 19205 SG CYS F 83 74.184 67.403 78.945 1.00103.76 S ATOM 16276 SG CYS G 104 49.742 59.485 76.913 1.00107.92 S ATOM 16282 SG CYS G 105 52.231 57.172 78.143 1.00105.62 S ATOM 22303 SG CYS H 83 53.576 60.290 78.918 1.00103.76 S ATOM 16107 SG CYS G 83 67.439 53.487 78.956 1.00103.76 S ATOM 19374 SG CYS F 104 68.180 49.708 76.898 1.00107.92 S ATOM 19380 SG CYS F 105 70.495 52.197 78.127 1.00105.62 S ATOM 13009 SG CYS E 83 60.309 74.305 78.915 1.00103.76 S ATOM 22472 SG CYS H 104 59.488 78.014 76.865 1.00107.92 S ATOM 22478 SG CYS H 105 57.187 75.514 78.096 1.00105.62 S Time building chain proxies: 13.29, per 1000 atoms: 0.52 Number of scatterers: 25404 At special positions: 0 Unit cell: (128.52, 128.52, 233.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 K 8 19.00 S 136 16.00 P 16 15.00 O 4372 8.00 N 4216 7.00 C 16648 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: 10.18 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 603 " pdb="ZN ZN A 603 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A 603 " - pdb=" SG CYS B 83 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 104 " pdb="ZN ZN A 603 " - pdb=" SG CYS A 105 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 601 " - pdb=" SG CYS C 83 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 104 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 105 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 77 " pdb="ZN ZN C 603 " - pdb=" SG CYS D 83 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 104 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 105 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" ND1 HIS D 77 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 104 " pdb="ZN ZN D 601 " - pdb=" SG CYS A 83 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 105 " pdb=" ZN E 603 " pdb="ZN ZN E 603 " - pdb=" ND1 HIS E 77 " pdb="ZN ZN E 603 " - pdb=" SG CYS F 83 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 104 " pdb="ZN ZN E 603 " - pdb=" SG CYS E 105 " pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" ND1 HIS F 77 " pdb="ZN ZN F 601 " - pdb=" SG CYS G 83 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 104 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 105 " pdb=" ZN G 603 " pdb="ZN ZN G 603 " - pdb=" ND1 HIS G 77 " pdb="ZN ZN G 603 " - pdb=" SG CYS H 83 " pdb="ZN ZN G 603 " - pdb=" SG CYS G 104 " pdb="ZN ZN G 603 " - pdb=" SG CYS G 105 " pdb=" ZN H 601 " pdb="ZN ZN H 601 " - pdb=" ND1 HIS H 77 " pdb="ZN ZN H 601 " - pdb=" SG CYS E 83 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 104 " pdb="ZN ZN H 601 " - pdb=" SG CYS H 105 " Number of angles added : 24 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 152 helices and 16 sheets defined 63.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.39 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 61 through 73 removed outlier: 4.313A pdb=" N HIS A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 103 through 109 removed outlier: 3.567A pdb=" N TRP A 106 " --> pdb=" O PRO A 103 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N MET A 107 " --> pdb=" O CYS A 104 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR A 108 " --> pdb=" O CYS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.206A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 187 through 210 Processing helix chain 'A' and resid 243 through 265 Processing helix chain 'A' and resid 270 through 275 Processing helix chain 'A' and resid 277 through 294 Proline residue: A 288 - end of helix removed outlier: 3.812A pdb=" N GLU A 292 " --> pdb=" O PRO A 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 327 removed outlier: 3.885A pdb=" N ASP A 305 " --> pdb=" O LYS A 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE A 321 " --> pdb=" O ARG A 317 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N HIS A 327 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 342 through 366 Processing helix chain 'A' and resid 387 through 398 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 61 through 73 removed outlier: 4.314A pdb=" N HIS C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 103 through 109 removed outlier: 3.567A pdb=" N TRP C 106 " --> pdb=" O PRO C 103 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N MET C 107 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR C 108 " --> pdb=" O CYS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 118 Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.207A pdb=" N LEU C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 187 through 210 Processing helix chain 'C' and resid 243 through 265 Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 277 through 294 Proline residue: C 288 - end of helix removed outlier: 3.812A pdb=" N GLU C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY C 294 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 327 removed outlier: 3.885A pdb=" N ASP C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL C 316 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG C 320 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE C 321 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE C 322 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N HIS C 327 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 342 through 366 Processing helix chain 'C' and resid 387 through 398 Processing helix chain 'C' and resid 411 through 429 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 61 through 73 removed outlier: 4.314A pdb=" N HIS B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 103 through 109 removed outlier: 3.567A pdb=" N TRP B 106 " --> pdb=" O PRO B 103 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET B 107 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR B 108 " --> pdb=" O CYS B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.206A pdb=" N LEU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 187 through 210 Processing helix chain 'B' and resid 243 through 265 Processing helix chain 'B' and resid 270 through 275 Processing helix chain 'B' and resid 277 through 294 Proline residue: B 288 - end of helix removed outlier: 3.811A pdb=" N GLU B 292 " --> pdb=" O PRO B 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 294 " --> pdb=" O TYR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 327 removed outlier: 3.885A pdb=" N ASP B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 312 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL B 316 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU B 319 " --> pdb=" O PHE B 315 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ARG B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE B 321 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N HIS B 327 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 340 Processing helix chain 'B' and resid 342 through 366 Processing helix chain 'B' and resid 387 through 398 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'D' and resid 23 through 28 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 61 through 73 removed outlier: 4.314A pdb=" N HIS D 66 " --> pdb=" O GLY D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.567A pdb=" N TRP D 106 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N MET D 107 " --> pdb=" O CYS D 104 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR D 108 " --> pdb=" O CYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 118 Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.207A pdb=" N LEU D 179 " --> pdb=" O ARG D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 187 through 210 Processing helix chain 'D' and resid 243 through 265 Processing helix chain 'D' and resid 270 through 275 Processing helix chain 'D' and resid 277 through 294 Proline residue: D 288 - end of helix removed outlier: 3.811A pdb=" N GLU D 292 " --> pdb=" O PRO D 288 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY D 294 " --> pdb=" O TYR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 327 removed outlier: 3.885A pdb=" N ASP D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL D 316 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE D 318 " --> pdb=" O ARG D 314 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU D 319 " --> pdb=" O PHE D 315 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG D 320 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE D 321 " --> pdb=" O ARG D 317 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE D 322 " --> pdb=" O ILE D 318 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N HIS D 327 " --> pdb=" O LYS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 340 Processing helix chain 'D' and resid 342 through 366 Processing helix chain 'D' and resid 387 through 398 Processing helix chain 'D' and resid 411 through 429 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'E' and resid 23 through 28 Processing helix chain 'E' and resid 33 through 38 Processing helix chain 'E' and resid 61 through 73 removed outlier: 4.314A pdb=" N HIS E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 94 Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 103 through 109 removed outlier: 3.567A pdb=" N TRP E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET E 107 " --> pdb=" O CYS E 104 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR E 108 " --> pdb=" O CYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 173 through 179 removed outlier: 4.207A pdb=" N LEU E 179 " --> pdb=" O ARG E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 187 through 210 Processing helix chain 'E' and resid 243 through 265 Processing helix chain 'E' and resid 270 through 275 Processing helix chain 'E' and resid 277 through 294 Proline residue: E 288 - end of helix removed outlier: 3.812A pdb=" N GLU E 292 " --> pdb=" O PRO E 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL E 293 " --> pdb=" O PHE E 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY E 294 " --> pdb=" O TYR E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 327 removed outlier: 3.884A pdb=" N ASP E 305 " --> pdb=" O LYS E 301 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL E 312 " --> pdb=" O GLY E 308 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL E 316 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG E 317 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE E 318 " --> pdb=" O ARG E 314 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG E 320 " --> pdb=" O VAL E 316 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE E 321 " --> pdb=" O ARG E 317 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS E 323 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU E 324 " --> pdb=" O ARG E 320 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N HIS E 327 " --> pdb=" O LYS E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 340 Processing helix chain 'E' and resid 342 through 366 Processing helix chain 'E' and resid 387 through 398 Processing helix chain 'E' and resid 411 through 429 Processing helix chain 'E' and resid 432 through 451 Processing helix chain 'G' and resid 23 through 28 Processing helix chain 'G' and resid 33 through 38 Processing helix chain 'G' and resid 61 through 73 removed outlier: 4.314A pdb=" N HIS G 66 " --> pdb=" O GLY G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 94 Processing helix chain 'G' and resid 98 through 100 No H-bonds generated for 'chain 'G' and resid 98 through 100' Processing helix chain 'G' and resid 103 through 109 removed outlier: 3.567A pdb=" N TRP G 106 " --> pdb=" O PRO G 103 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET G 107 " --> pdb=" O CYS G 104 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR G 108 " --> pdb=" O CYS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 118 Processing helix chain 'G' and resid 173 through 179 removed outlier: 4.206A pdb=" N LEU G 179 " --> pdb=" O ARG G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 187 through 210 Processing helix chain 'G' and resid 243 through 265 Processing helix chain 'G' and resid 270 through 275 Processing helix chain 'G' and resid 277 through 294 Proline residue: G 288 - end of helix removed outlier: 3.811A pdb=" N GLU G 292 " --> pdb=" O PRO G 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL G 293 " --> pdb=" O PHE G 289 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLY G 294 " --> pdb=" O TYR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 327 removed outlier: 3.884A pdb=" N ASP G 305 " --> pdb=" O LYS G 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL G 312 " --> pdb=" O GLY G 308 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL G 316 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE G 318 " --> pdb=" O ARG G 314 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU G 319 " --> pdb=" O PHE G 315 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG G 320 " --> pdb=" O VAL G 316 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE G 321 " --> pdb=" O ARG G 317 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE G 322 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYS G 323 " --> pdb=" O LEU G 319 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU G 324 " --> pdb=" O ARG G 320 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N HIS G 327 " --> pdb=" O LYS G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 329 through 340 Processing helix chain 'G' and resid 342 through 366 Processing helix chain 'G' and resid 387 through 398 Processing helix chain 'G' and resid 411 through 429 Processing helix chain 'G' and resid 432 through 451 Processing helix chain 'F' and resid 23 through 28 Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 61 through 73 removed outlier: 4.314A pdb=" N HIS F 66 " --> pdb=" O GLY F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 94 Processing helix chain 'F' and resid 98 through 100 No H-bonds generated for 'chain 'F' and resid 98 through 100' Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.568A pdb=" N TRP F 106 " --> pdb=" O PRO F 103 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N MET F 107 " --> pdb=" O CYS F 104 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR F 108 " --> pdb=" O CYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 118 Processing helix chain 'F' and resid 173 through 179 removed outlier: 4.207A pdb=" N LEU F 179 " --> pdb=" O ARG F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 187 through 210 Processing helix chain 'F' and resid 243 through 265 Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 277 through 294 Proline residue: F 288 - end of helix removed outlier: 3.812A pdb=" N GLU F 292 " --> pdb=" O PRO F 288 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL F 293 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY F 294 " --> pdb=" O TYR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 327 removed outlier: 3.885A pdb=" N ASP F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL F 312 " --> pdb=" O GLY F 308 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL F 316 " --> pdb=" O VAL F 312 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG F 317 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE F 318 " --> pdb=" O ARG F 314 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG F 320 " --> pdb=" O VAL F 316 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE F 321 " --> pdb=" O ARG F 317 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N PHE F 322 " --> pdb=" O ILE F 318 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS F 323 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N HIS F 327 " --> pdb=" O LYS F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 340 Processing helix chain 'F' and resid 342 through 366 Processing helix chain 'F' and resid 387 through 398 Processing helix chain 'F' and resid 411 through 429 Processing helix chain 'F' and resid 432 through 451 Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 33 through 38 Processing helix chain 'H' and resid 61 through 73 removed outlier: 4.313A pdb=" N HIS H 66 " --> pdb=" O GLY H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 94 Processing helix chain 'H' and resid 98 through 100 No H-bonds generated for 'chain 'H' and resid 98 through 100' Processing helix chain 'H' and resid 103 through 109 removed outlier: 3.568A pdb=" N TRP H 106 " --> pdb=" O PRO H 103 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N MET H 107 " --> pdb=" O CYS H 104 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N THR H 108 " --> pdb=" O CYS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 118 Processing helix chain 'H' and resid 173 through 179 removed outlier: 4.207A pdb=" N LEU H 179 " --> pdb=" O ARG H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 187 through 210 Processing helix chain 'H' and resid 243 through 265 Processing helix chain 'H' and resid 270 through 275 Processing helix chain 'H' and resid 277 through 294 Proline residue: H 288 - end of helix removed outlier: 3.811A pdb=" N GLU H 292 " --> pdb=" O PRO H 288 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N VAL H 293 " --> pdb=" O PHE H 289 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY H 294 " --> pdb=" O TYR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 327 removed outlier: 3.885A pdb=" N ASP H 305 " --> pdb=" O LYS H 301 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL H 312 " --> pdb=" O GLY H 308 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N VAL H 316 " --> pdb=" O VAL H 312 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG H 317 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE H 318 " --> pdb=" O ARG H 314 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU H 319 " --> pdb=" O PHE H 315 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG H 320 " --> pdb=" O VAL H 316 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE H 321 " --> pdb=" O ARG H 317 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N PHE H 322 " --> pdb=" O ILE H 318 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS H 323 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU H 324 " --> pdb=" O ARG H 320 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N HIS H 327 " --> pdb=" O LYS H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 329 through 340 Processing helix chain 'H' and resid 342 through 366 Processing helix chain 'H' and resid 387 through 398 Processing helix chain 'H' and resid 411 through 429 Processing helix chain 'H' and resid 432 through 451 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 22 Processing sheet with id= B, first strand: chain 'A' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU A 238 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 17 through 22 Processing sheet with id= D, first strand: chain 'C' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU C 238 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 17 through 22 Processing sheet with id= F, first strand: chain 'B' and resid 218 through 221 removed outlier: 3.753A pdb=" N GLU B 238 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 17 through 22 Processing sheet with id= H, first strand: chain 'D' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU D 238 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 17 through 22 Processing sheet with id= J, first strand: chain 'E' and resid 218 through 221 removed outlier: 3.753A pdb=" N GLU E 238 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 17 through 22 Processing sheet with id= L, first strand: chain 'G' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU G 238 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 17 through 22 Processing sheet with id= N, first strand: chain 'F' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU F 238 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 17 through 22 Processing sheet with id= P, first strand: chain 'H' and resid 218 through 221 removed outlier: 3.754A pdb=" N GLU H 238 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 10.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3860 1.31 - 1.43: 7607 1.43 - 1.56: 14381 1.56 - 1.68: 48 1.68 - 1.81: 208 Bond restraints: 26104 Sorted by residual: bond pdb=" N PCF C 602 " pdb=" C12 PCF C 602 " ideal model delta sigma weight residual 1.447 1.476 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" N PCF H 603 " pdb=" C12 PCF H 603 " ideal model delta sigma weight residual 1.447 1.476 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" N PCF G 602 " pdb=" C12 PCF G 602 " ideal model delta sigma weight residual 1.447 1.476 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" N PCF A 602 " pdb=" C12 PCF A 602 " ideal model delta sigma weight residual 1.447 1.476 -0.029 2.00e-02 2.50e+03 2.03e+00 bond pdb=" N PCF D 603 " pdb=" C12 PCF D 603 " ideal model delta sigma weight residual 1.447 1.476 -0.029 2.00e-02 2.50e+03 2.03e+00 ... (remaining 26099 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.26: 1105 107.26 - 113.94: 14702 113.94 - 120.63: 11003 120.63 - 127.32: 8286 127.32 - 134.01: 408 Bond angle restraints: 35504 Sorted by residual: angle pdb=" CA LYS A 456 " pdb=" CB LYS A 456 " pdb=" CG LYS A 456 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA LYS D 456 " pdb=" CB LYS D 456 " pdb=" CG LYS D 456 " ideal model delta sigma weight residual 114.10 120.08 -5.98 2.00e+00 2.50e-01 8.95e+00 angle pdb=" CA LEU D 91 " pdb=" CB LEU D 91 " pdb=" CG LEU D 91 " ideal model delta sigma weight residual 116.30 125.79 -9.49 3.50e+00 8.16e-02 7.36e+00 angle pdb=" CA LEU E 91 " pdb=" CB LEU E 91 " pdb=" CG LEU E 91 " ideal model delta sigma weight residual 116.30 125.79 -9.49 3.50e+00 8.16e-02 7.35e+00 angle pdb=" CA LEU F 91 " pdb=" CB LEU F 91 " pdb=" CG LEU F 91 " ideal model delta sigma weight residual 116.30 125.77 -9.47 3.50e+00 8.16e-02 7.33e+00 ... (remaining 35499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 13958 16.96 - 33.92: 831 33.92 - 50.89: 226 50.89 - 67.85: 105 67.85 - 84.81: 40 Dihedral angle restraints: 15160 sinusoidal: 5996 harmonic: 9164 Sorted by residual: dihedral pdb=" CA ASP E 305 " pdb=" CB ASP E 305 " pdb=" CG ASP E 305 " pdb=" OD1 ASP E 305 " ideal model delta sinusoidal sigma weight residual -30.00 -83.69 53.69 1 2.00e+01 2.50e-03 9.79e+00 dihedral pdb=" CA ASP C 305 " pdb=" CB ASP C 305 " pdb=" CG ASP C 305 " pdb=" OD1 ASP C 305 " ideal model delta sinusoidal sigma weight residual -30.00 -83.69 53.69 1 2.00e+01 2.50e-03 9.79e+00 dihedral pdb=" CA ASP H 305 " pdb=" CB ASP H 305 " pdb=" CG ASP H 305 " pdb=" OD1 ASP H 305 " ideal model delta sinusoidal sigma weight residual -30.00 -83.67 53.67 1 2.00e+01 2.50e-03 9.78e+00 ... (remaining 15157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2670 0.037 - 0.074: 909 0.074 - 0.110: 297 0.110 - 0.147: 16 0.147 - 0.184: 8 Chirality restraints: 3900 Sorted by residual: chirality pdb=" C2 PCF G 602 " pdb=" C1 PCF G 602 " pdb=" C3 PCF G 602 " pdb=" O21 PCF G 602 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" C2 PCF A 602 " pdb=" C1 PCF A 602 " pdb=" C3 PCF A 602 " pdb=" O21 PCF A 602 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.18 2.00e-01 2.50e+01 8.36e-01 chirality pdb=" C2 PCF E 602 " pdb=" C1 PCF E 602 " pdb=" C3 PCF E 602 " pdb=" O21 PCF E 602 " both_signs ideal model delta sigma weight residual False -2.53 -2.35 -0.18 2.00e-01 2.50e+01 8.35e-01 ... (remaining 3897 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL H 432 " -0.031 5.00e-02 4.00e+02 4.61e-02 3.39e+00 pdb=" N PRO H 433 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO H 433 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 433 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 432 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO C 433 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 433 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 433 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 432 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO E 433 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 433 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 433 " -0.026 5.00e-02 4.00e+02 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 8372 2.84 - 3.42: 28527 3.42 - 3.99: 45551 3.99 - 4.57: 67039 4.57 - 5.14: 95254 Nonbonded interactions: 244743 Sorted by model distance: nonbonded pdb=" OH TYR A 48 " pdb=" OD1 ASP A 53 " model vdw 2.269 2.440 nonbonded pdb=" OH TYR F 48 " pdb=" OD1 ASP F 53 " model vdw 2.269 2.440 nonbonded pdb=" OH TYR C 48 " pdb=" OD1 ASP C 53 " model vdw 2.269 2.440 nonbonded pdb=" OH TYR E 48 " pdb=" OD1 ASP E 53 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR B 48 " pdb=" OD1 ASP B 53 " model vdw 2.270 2.440 ... (remaining 244738 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' and (resid 7 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or resid 457 through 463)) selection = (chain 'B' and (resid 7 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or resid 457 through 463)) selection = (chain 'C' and (resid 7 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or resid 457 through 463)) selection = (chain 'D' and (resid 7 through 455 or (resid 456 and (name N or name CA or name \ C or name O or name CB )) or resid 457 through 463)) selection = (chain 'E' and resid 7 through 463) selection = (chain 'F' and resid 7 through 463) selection = (chain 'G' and resid 7 through 463) selection = (chain 'H' and resid 7 through 463) } 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: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 21.030 Check model and map are aligned: 0.480 Set scattering table: 0.240 Process input model: 74.260 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 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 : 0.004 0.043 26104 Z= 0.258 Angle : 0.545 9.493 35504 Z= 0.299 Chirality : 0.040 0.184 3900 Planarity : 0.005 0.046 4432 Dihedral : 13.846 84.811 9216 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.53 % Allowed : 6.76 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.13), residues: 3076 helix: -0.05 (0.11), residues: 1928 sheet: None (None), residues: 0 loop : -1.38 (0.15), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 94 HIS 0.005 0.001 HIS G 112 PHE 0.009 0.001 PHE E 64 TYR 0.010 0.001 TYR C 70 ARG 0.003 0.001 ARG H 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 523 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7350 (t70) cc_final: 0.6961 (t0) REVERT: A 190 ARG cc_start: 0.5286 (ttt90) cc_final: 0.4708 (tmm160) REVERT: A 194 PHE cc_start: 0.7027 (m-80) cc_final: 0.6769 (m-10) REVERT: A 238 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6182 (pm20) REVERT: A 276 ASN cc_start: 0.7636 (t0) cc_final: 0.7430 (t0) REVERT: A 442 TYR cc_start: 0.7715 (m-10) cc_final: 0.7356 (m-80) REVERT: A 447 MET cc_start: 0.7411 (mmt) cc_final: 0.7118 (mmm) REVERT: A 458 LYS cc_start: 0.6687 (mmtp) cc_final: 0.6341 (mtpt) REVERT: C 53 ASP cc_start: 0.7335 (t70) cc_final: 0.6988 (t0) REVERT: C 190 ARG cc_start: 0.5148 (ttt90) cc_final: 0.4439 (tmm160) REVERT: C 199 PHE cc_start: 0.7693 (m-80) cc_final: 0.7101 (m-80) REVERT: C 238 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6247 (pm20) REVERT: C 406 MET cc_start: 0.8331 (ptp) cc_final: 0.8076 (ptp) REVERT: C 458 LYS cc_start: 0.6717 (mmtp) cc_final: 0.6364 (mtpt) REVERT: B 40 PRO cc_start: 0.7668 (Cg_endo) cc_final: 0.7449 (Cg_exo) REVERT: B 53 ASP cc_start: 0.7420 (t70) cc_final: 0.7052 (t0) REVERT: B 190 ARG cc_start: 0.5128 (ttt90) cc_final: 0.4648 (tmm160) REVERT: B 194 PHE cc_start: 0.7024 (m-80) cc_final: 0.6711 (m-10) REVERT: B 199 PHE cc_start: 0.7592 (m-80) cc_final: 0.6892 (m-80) REVERT: B 238 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6307 (pm20) REVERT: B 406 MET cc_start: 0.8361 (ptp) cc_final: 0.8112 (ptp) REVERT: B 442 TYR cc_start: 0.7645 (m-10) cc_final: 0.7304 (m-80) REVERT: B 461 PRO cc_start: 0.8866 (Cg_endo) cc_final: 0.8651 (Cg_exo) REVERT: D 40 PRO cc_start: 0.7553 (Cg_endo) cc_final: 0.7290 (Cg_exo) REVERT: D 53 ASP cc_start: 0.7344 (t70) cc_final: 0.6923 (t0) REVERT: D 190 ARG cc_start: 0.5377 (ttt90) cc_final: 0.4692 (tmm160) REVERT: D 194 PHE cc_start: 0.6935 (m-80) cc_final: 0.6704 (m-10) REVERT: D 238 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6296 (pm20) REVERT: D 447 MET cc_start: 0.7397 (mmt) cc_final: 0.7183 (mmm) REVERT: D 458 LYS cc_start: 0.6667 (mmtp) cc_final: 0.6043 (mmtt) REVERT: E 89 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: G 53 ASP cc_start: 0.6759 (t70) cc_final: 0.6450 (t0) REVERT: G 89 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.6199 (tm-30) REVERT: G 278 LEU cc_start: 0.5546 (mp) cc_final: 0.5138 (tt) REVERT: G 321 ILE cc_start: 0.7493 (tp) cc_final: 0.7275 (tt) REVERT: F 89 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6217 (tm-30) REVERT: H 41 ASP cc_start: 0.6397 (m-30) cc_final: 0.6189 (t0) REVERT: H 45 HIS cc_start: 0.6252 (m170) cc_final: 0.5874 (m170) REVERT: H 89 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6156 (tm-30) outliers start: 64 outliers final: 12 residues processed: 574 average time/residue: 0.4219 time to fit residues: 359.8610 Evaluate side-chains 331 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 311 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 282 ASP Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 329 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 0.0870 chunk 283 optimal weight: 3.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS C 327 HIS E 19 HIS E 279 ASN G 19 HIS G 279 ASN F 19 HIS F 279 ASN H 19 HIS H 279 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26104 Z= 0.202 Angle : 0.537 8.735 35504 Z= 0.261 Chirality : 0.041 0.181 3900 Planarity : 0.005 0.049 4432 Dihedral : 10.568 80.726 3834 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.69 % Allowed : 9.93 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3076 helix: 1.29 (0.12), residues: 1864 sheet: -0.92 (0.47), residues: 112 loop : -0.42 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 255 HIS 0.003 0.001 HIS G 112 PHE 0.018 0.001 PHE G 283 TYR 0.009 0.001 TYR D 109 ARG 0.008 0.000 ARG G 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 347 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7833 (ptt180) cc_final: 0.6623 (mtt180) REVERT: A 53 ASP cc_start: 0.7251 (t70) cc_final: 0.6993 (t0) REVERT: A 190 ARG cc_start: 0.5320 (ttt90) cc_final: 0.4820 (tmm160) REVERT: A 194 PHE cc_start: 0.7100 (m-80) cc_final: 0.6817 (m-10) REVERT: A 238 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6580 (pm20) REVERT: A 442 TYR cc_start: 0.7690 (m-10) cc_final: 0.7403 (m-80) REVERT: C 53 ASP cc_start: 0.7262 (t70) cc_final: 0.7042 (t0) REVERT: C 190 ARG cc_start: 0.5191 (ttt90) cc_final: 0.4448 (tmm160) REVERT: C 199 PHE cc_start: 0.7678 (m-80) cc_final: 0.7109 (m-10) REVERT: C 238 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6614 (pm20) REVERT: C 406 MET cc_start: 0.8510 (ptp) cc_final: 0.8189 (ptm) REVERT: C 447 MET cc_start: 0.7414 (mmt) cc_final: 0.7160 (mmm) REVERT: B 9 ARG cc_start: 0.7887 (ptt180) cc_final: 0.6662 (mtt180) REVERT: B 53 ASP cc_start: 0.7295 (t70) cc_final: 0.7052 (t0) REVERT: B 190 ARG cc_start: 0.5153 (ttt90) cc_final: 0.4605 (tmm160) REVERT: B 199 PHE cc_start: 0.7658 (m-80) cc_final: 0.6732 (m-10) REVERT: B 238 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6604 (pm20) REVERT: B 323 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8751 (ttpp) REVERT: B 406 MET cc_start: 0.8475 (ptp) cc_final: 0.7980 (ptm) REVERT: B 442 TYR cc_start: 0.7726 (m-10) cc_final: 0.7348 (m-80) REVERT: D 9 ARG cc_start: 0.7836 (ptt180) cc_final: 0.6713 (mtt180) REVERT: D 53 ASP cc_start: 0.7223 (t70) cc_final: 0.6936 (t0) REVERT: D 190 ARG cc_start: 0.5418 (ttt90) cc_final: 0.4815 (tmm160) REVERT: D 194 PHE cc_start: 0.6952 (m-80) cc_final: 0.6653 (m-10) REVERT: D 199 PHE cc_start: 0.7611 (m-80) cc_final: 0.7115 (m-10) REVERT: D 238 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6741 (pm20) REVERT: D 244 PHE cc_start: 0.7013 (m-80) cc_final: 0.6717 (t80) REVERT: E 53 ASP cc_start: 0.6728 (t0) cc_final: 0.6506 (t0) REVERT: E 89 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6079 (tm-30) REVERT: E 107 MET cc_start: 0.8235 (mmm) cc_final: 0.7921 (mmm) REVERT: E 197 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.6033 (tt) REVERT: G 89 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.6164 (tm-30) REVERT: G 197 LEU cc_start: 0.5866 (OUTLIER) cc_final: 0.5402 (tt) REVERT: G 321 ILE cc_start: 0.7355 (tp) cc_final: 0.7083 (tt) REVERT: G 331 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7809 (mm) REVERT: F 53 ASP cc_start: 0.6794 (t0) cc_final: 0.6586 (t0) REVERT: F 89 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.6155 (tm-30) REVERT: F 107 MET cc_start: 0.8255 (mmm) cc_final: 0.8043 (mmm) REVERT: F 197 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5299 (tt) REVERT: F 331 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7817 (mm) REVERT: F 345 PHE cc_start: 0.7952 (m-80) cc_final: 0.7700 (m-80) REVERT: H 41 ASP cc_start: 0.6363 (m-30) cc_final: 0.6128 (t0) REVERT: H 45 HIS cc_start: 0.6266 (m170) cc_final: 0.5950 (m170) REVERT: H 89 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.6205 (tm-30) REVERT: H 107 MET cc_start: 0.8287 (mmm) cc_final: 0.7977 (mmm) REVERT: H 197 LEU cc_start: 0.5393 (OUTLIER) cc_final: 0.4954 (tt) REVERT: H 321 ILE cc_start: 0.7337 (tp) cc_final: 0.7058 (tt) REVERT: H 449 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6891 (mtpp) outliers start: 68 outliers final: 36 residues processed: 397 average time/residue: 0.3929 time to fit residues: 239.4033 Evaluate side-chains 345 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 293 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 HIS Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 238 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 238 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 449 LYS Chi-restraints excluded: chain H residue 451 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.0370 chunk 235 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 306 optimal weight: 5.9990 chunk 252 optimal weight: 20.0000 chunk 281 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 227 optimal weight: 0.9990 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN E 381 HIS ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 HIS H 381 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5897 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26104 Z= 0.203 Angle : 0.518 9.490 35504 Z= 0.251 Chirality : 0.041 0.262 3900 Planarity : 0.004 0.041 4432 Dihedral : 9.475 74.664 3826 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.97 % Allowed : 12.14 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.15), residues: 3076 helix: 1.39 (0.12), residues: 1904 sheet: -0.49 (0.73), residues: 56 loop : -0.27 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 255 HIS 0.004 0.001 HIS G 336 PHE 0.022 0.001 PHE H 283 TYR 0.008 0.001 TYR F 48 ARG 0.006 0.000 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 308 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7896 (ptt180) cc_final: 0.6665 (mtt180) REVERT: A 53 ASP cc_start: 0.7234 (t70) cc_final: 0.6918 (t0) REVERT: A 190 ARG cc_start: 0.5318 (ttt90) cc_final: 0.4796 (tmm160) REVERT: A 194 PHE cc_start: 0.7086 (m-80) cc_final: 0.6788 (m-10) REVERT: A 199 PHE cc_start: 0.7548 (m-80) cc_final: 0.7199 (m-10) REVERT: A 238 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6530 (pm20) REVERT: C 53 ASP cc_start: 0.7197 (t70) cc_final: 0.6975 (t0) REVERT: C 190 ARG cc_start: 0.5202 (ttt90) cc_final: 0.4420 (tmm160) REVERT: C 199 PHE cc_start: 0.7647 (m-80) cc_final: 0.7105 (m-10) REVERT: C 406 MET cc_start: 0.8533 (ptp) cc_final: 0.8028 (ptm) REVERT: B 9 ARG cc_start: 0.7926 (ptt180) cc_final: 0.6743 (mtt180) REVERT: B 53 ASP cc_start: 0.7285 (t70) cc_final: 0.7064 (t0) REVERT: B 190 ARG cc_start: 0.5156 (ttt90) cc_final: 0.4628 (tmm160) REVERT: B 199 PHE cc_start: 0.7402 (m-80) cc_final: 0.7012 (m-10) REVERT: B 458 LYS cc_start: 0.6149 (mtmt) cc_final: 0.5905 (mttm) REVERT: D 9 ARG cc_start: 0.7861 (ptt180) cc_final: 0.6668 (mtt180) REVERT: D 45 HIS cc_start: 0.7555 (m90) cc_final: 0.7274 (m90) REVERT: D 53 ASP cc_start: 0.7262 (t70) cc_final: 0.6997 (t0) REVERT: D 190 ARG cc_start: 0.5468 (ttt90) cc_final: 0.4842 (tmm160) REVERT: D 194 PHE cc_start: 0.6968 (m-80) cc_final: 0.6660 (m-10) REVERT: D 199 PHE cc_start: 0.7662 (m-80) cc_final: 0.7272 (m-80) REVERT: D 238 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6602 (pm20) REVERT: D 244 PHE cc_start: 0.7027 (m-80) cc_final: 0.6759 (t80) REVERT: E 53 ASP cc_start: 0.7052 (t0) cc_final: 0.6835 (t0) REVERT: E 89 GLU cc_start: 0.6422 (tt0) cc_final: 0.6144 (tm-30) REVERT: E 315 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.6243 (t80) REVERT: G 89 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: G 107 MET cc_start: 0.8121 (mmm) cc_final: 0.7818 (mmm) REVERT: G 315 PHE cc_start: 0.6678 (OUTLIER) cc_final: 0.6159 (t80) REVERT: G 321 ILE cc_start: 0.7414 (tp) cc_final: 0.7185 (tt) REVERT: F 53 ASP cc_start: 0.7062 (t0) cc_final: 0.6854 (t0) REVERT: F 89 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6184 (tm-30) REVERT: F 315 PHE cc_start: 0.6436 (OUTLIER) cc_final: 0.6086 (t80) REVERT: F 331 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7790 (mm) REVERT: H 45 HIS cc_start: 0.6282 (m170) cc_final: 0.6017 (m170) REVERT: H 89 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6172 (tm-30) outliers start: 75 outliers final: 50 residues processed: 362 average time/residue: 0.3684 time to fit residues: 206.5160 Evaluate side-chains 341 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 282 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 238 GLU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 89 GLU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 315 PHE Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 20.0000 chunk 147 optimal weight: 0.2980 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 284 optimal weight: 0.0870 chunk 301 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 269 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.4362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN E 220 ASN ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5928 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26104 Z= 0.254 Angle : 0.537 10.971 35504 Z= 0.262 Chirality : 0.042 0.361 3900 Planarity : 0.005 0.044 4432 Dihedral : 8.789 65.162 3817 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.85 % Allowed : 13.77 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.15), residues: 3076 helix: 1.28 (0.12), residues: 1968 sheet: 0.09 (0.64), residues: 72 loop : -0.14 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 255 HIS 0.007 0.001 HIS F 45 PHE 0.016 0.001 PHE G 199 TYR 0.019 0.001 TYR G 365 ARG 0.006 0.000 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 309 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 HIS cc_start: 0.7685 (m90) cc_final: 0.7467 (m90) REVERT: A 53 ASP cc_start: 0.7267 (t70) cc_final: 0.7065 (t0) REVERT: A 190 ARG cc_start: 0.5392 (ttt90) cc_final: 0.4823 (tmm160) REVERT: A 194 PHE cc_start: 0.7190 (m-80) cc_final: 0.6861 (m-10) REVERT: A 199 PHE cc_start: 0.7538 (m-80) cc_final: 0.7227 (m-10) REVERT: C 9 ARG cc_start: 0.7894 (ptt180) cc_final: 0.6727 (mtt90) REVERT: C 53 ASP cc_start: 0.7262 (t70) cc_final: 0.6938 (t0) REVERT: C 190 ARG cc_start: 0.5252 (ttt90) cc_final: 0.4400 (tmm160) REVERT: C 199 PHE cc_start: 0.7581 (m-80) cc_final: 0.7090 (m-10) REVERT: C 406 MET cc_start: 0.8688 (ptp) cc_final: 0.8375 (ptm) REVERT: B 53 ASP cc_start: 0.7342 (t70) cc_final: 0.7038 (t0) REVERT: B 190 ARG cc_start: 0.5274 (ttt90) cc_final: 0.4842 (tmm160) REVERT: B 199 PHE cc_start: 0.7580 (m-80) cc_final: 0.6861 (m-10) REVERT: B 255 TRP cc_start: 0.7804 (t-100) cc_final: 0.7554 (t60) REVERT: B 458 LYS cc_start: 0.6223 (mtmt) cc_final: 0.5904 (mttm) REVERT: D 53 ASP cc_start: 0.7252 (t70) cc_final: 0.7025 (t0) REVERT: D 190 ARG cc_start: 0.5508 (ttt90) cc_final: 0.4830 (tmm160) REVERT: D 194 PHE cc_start: 0.7008 (m-80) cc_final: 0.6678 (m-10) REVERT: D 199 PHE cc_start: 0.7661 (m-80) cc_final: 0.7132 (m-80) REVERT: D 273 PHE cc_start: 0.6104 (t80) cc_final: 0.5874 (t80) REVERT: D 327 HIS cc_start: 0.7990 (m-70) cc_final: 0.7741 (m-70) REVERT: E 53 ASP cc_start: 0.7189 (t0) cc_final: 0.6835 (t0) REVERT: E 89 GLU cc_start: 0.6304 (tt0) cc_final: 0.6062 (tm-30) REVERT: G 197 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5264 (tt) REVERT: G 321 ILE cc_start: 0.7444 (tp) cc_final: 0.7225 (tt) REVERT: F 53 ASP cc_start: 0.7157 (t0) cc_final: 0.6818 (t0) REVERT: H 321 ILE cc_start: 0.7382 (tp) cc_final: 0.7175 (tt) REVERT: H 331 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7695 (mm) outliers start: 72 outliers final: 38 residues processed: 363 average time/residue: 0.3987 time to fit residues: 219.7403 Evaluate side-chains 319 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 2.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 451 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 257 optimal weight: 6.9990 chunk 208 optimal weight: 0.0050 chunk 0 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 HIS ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN E 220 ASN E 336 HIS ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5929 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26104 Z= 0.246 Angle : 0.541 15.752 35504 Z= 0.262 Chirality : 0.041 0.358 3900 Planarity : 0.005 0.046 4432 Dihedral : 8.308 58.961 3798 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.12 % Allowed : 14.40 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.15), residues: 3076 helix: 1.28 (0.12), residues: 1968 sheet: -0.10 (0.62), residues: 72 loop : -0.07 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 255 HIS 0.005 0.001 HIS H 45 PHE 0.021 0.001 PHE H 315 TYR 0.013 0.001 TYR G 365 ARG 0.005 0.000 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 299 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7354 (t70) cc_final: 0.7150 (t0) REVERT: A 190 ARG cc_start: 0.5475 (ttt90) cc_final: 0.4920 (tmm160) REVERT: A 194 PHE cc_start: 0.7143 (m-80) cc_final: 0.6790 (m-10) REVERT: A 199 PHE cc_start: 0.7540 (m-80) cc_final: 0.7239 (m-10) REVERT: C 9 ARG cc_start: 0.7914 (ptt180) cc_final: 0.6674 (tpp80) REVERT: C 53 ASP cc_start: 0.7285 (t70) cc_final: 0.7070 (t0) REVERT: C 190 ARG cc_start: 0.5276 (ttt90) cc_final: 0.4392 (tmm160) REVERT: C 199 PHE cc_start: 0.7578 (m-80) cc_final: 0.7029 (m-10) REVERT: C 406 MET cc_start: 0.8651 (ptp) cc_final: 0.8394 (ptm) REVERT: B 9 ARG cc_start: 0.7888 (ptt180) cc_final: 0.6776 (mtt180) REVERT: B 53 ASP cc_start: 0.7264 (t70) cc_final: 0.7038 (t0) REVERT: B 190 ARG cc_start: 0.5341 (ttt90) cc_final: 0.4795 (tmm160) REVERT: B 199 PHE cc_start: 0.7525 (m-80) cc_final: 0.7093 (m-10) REVERT: B 213 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7412 (mp0) REVERT: B 323 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8758 (ttpp) REVERT: D 9 ARG cc_start: 0.7899 (ptt180) cc_final: 0.6801 (mtt180) REVERT: D 53 ASP cc_start: 0.7311 (t70) cc_final: 0.6970 (t0) REVERT: D 190 ARG cc_start: 0.5513 (ttt90) cc_final: 0.4769 (tmm160) REVERT: D 194 PHE cc_start: 0.6994 (m-80) cc_final: 0.6631 (m-10) REVERT: D 199 PHE cc_start: 0.7632 (m-80) cc_final: 0.7240 (m-10) REVERT: D 273 PHE cc_start: 0.6143 (t80) cc_final: 0.5916 (t80) REVERT: D 327 HIS cc_start: 0.8040 (m-70) cc_final: 0.7792 (m-70) REVERT: E 53 ASP cc_start: 0.7085 (t0) cc_final: 0.6798 (t0) REVERT: E 89 GLU cc_start: 0.6318 (tt0) cc_final: 0.6035 (tm-30) REVERT: E 321 ILE cc_start: 0.7410 (tp) cc_final: 0.7098 (tt) REVERT: E 449 LYS cc_start: 0.7406 (mmtt) cc_final: 0.6781 (ttpp) REVERT: G 197 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.5113 (tt) REVERT: G 321 ILE cc_start: 0.7425 (tp) cc_final: 0.7211 (tt) REVERT: F 53 ASP cc_start: 0.7106 (t0) cc_final: 0.6817 (t0) REVERT: F 321 ILE cc_start: 0.7366 (tp) cc_final: 0.7120 (tt) REVERT: F 331 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7741 (mm) REVERT: H 331 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7680 (mm) outliers start: 79 outliers final: 48 residues processed: 357 average time/residue: 0.3981 time to fit residues: 217.7727 Evaluate side-chains 329 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 277 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 10.0000 chunk 271 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 301 optimal weight: 9.9990 chunk 250 optimal weight: 30.0000 chunk 139 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 158 optimal weight: 0.0010 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 GLN B 383 HIS ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS E 45 HIS E 220 ASN G 45 HIS G 336 HIS ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 HIS H 336 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26104 Z= 0.383 Angle : 0.607 13.654 35504 Z= 0.298 Chirality : 0.044 0.344 3900 Planarity : 0.005 0.048 4432 Dihedral : 8.389 59.013 3797 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.77 % Allowed : 15.82 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.15), residues: 3076 helix: 1.13 (0.12), residues: 1928 sheet: -0.38 (0.61), residues: 72 loop : -0.04 (0.19), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 106 HIS 0.006 0.001 HIS H 77 PHE 0.022 0.002 PHE F 351 TYR 0.017 0.002 TYR C 70 ARG 0.004 0.000 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 280 time to evaluate : 2.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7957 (ptt180) cc_final: 0.6801 (mtt180) REVERT: A 53 ASP cc_start: 0.7394 (t70) cc_final: 0.7149 (t0) REVERT: A 190 ARG cc_start: 0.5573 (ttt90) cc_final: 0.4918 (tmm160) REVERT: A 194 PHE cc_start: 0.7216 (m-80) cc_final: 0.6830 (m-10) REVERT: A 199 PHE cc_start: 0.7561 (m-80) cc_final: 0.7280 (m-10) REVERT: C 9 ARG cc_start: 0.7943 (ptt180) cc_final: 0.6677 (tpp80) REVERT: C 53 ASP cc_start: 0.7341 (t70) cc_final: 0.7103 (t0) REVERT: C 190 ARG cc_start: 0.5378 (ttt90) cc_final: 0.4428 (tmm160) REVERT: C 199 PHE cc_start: 0.7676 (m-80) cc_final: 0.7140 (m-10) REVERT: C 406 MET cc_start: 0.8858 (ptp) cc_final: 0.8505 (ptp) REVERT: B 9 ARG cc_start: 0.7957 (ptt180) cc_final: 0.6744 (tpp80) REVERT: B 53 ASP cc_start: 0.7377 (t70) cc_final: 0.7130 (t0) REVERT: B 190 ARG cc_start: 0.5506 (ttt90) cc_final: 0.4770 (tmm160) REVERT: B 199 PHE cc_start: 0.7572 (m-80) cc_final: 0.7025 (t80) REVERT: B 323 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8760 (ttpp) REVERT: B 422 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8051 (mm) REVERT: D 9 ARG cc_start: 0.7966 (ptt180) cc_final: 0.6739 (tpp80) REVERT: D 53 ASP cc_start: 0.7378 (t70) cc_final: 0.7130 (t0) REVERT: D 190 ARG cc_start: 0.5584 (ttt90) cc_final: 0.4725 (tmm160) REVERT: D 194 PHE cc_start: 0.7168 (m-80) cc_final: 0.6722 (m-10) REVERT: D 199 PHE cc_start: 0.7647 (m-80) cc_final: 0.7307 (m-80) REVERT: D 327 HIS cc_start: 0.8131 (m-70) cc_final: 0.7830 (m-70) REVERT: E 89 GLU cc_start: 0.6285 (tt0) cc_final: 0.5999 (tm-30) REVERT: E 321 ILE cc_start: 0.7448 (tp) cc_final: 0.7241 (tt) REVERT: E 449 LYS cc_start: 0.7364 (mmtt) cc_final: 0.6763 (ttpp) REVERT: G 197 LEU cc_start: 0.5642 (OUTLIER) cc_final: 0.5230 (tt) REVERT: G 321 ILE cc_start: 0.7466 (tp) cc_final: 0.7247 (tt) REVERT: F 319 LEU cc_start: 0.7621 (mp) cc_final: 0.7135 (mt) REVERT: F 323 LYS cc_start: 0.7457 (mmtm) cc_final: 0.6972 (mmtt) REVERT: F 398 MET cc_start: 0.7646 (tpp) cc_final: 0.7304 (tpt) REVERT: H 331 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7790 (mm) REVERT: H 445 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7230 (tt) outliers start: 70 outliers final: 44 residues processed: 334 average time/residue: 0.4104 time to fit residues: 210.0834 Evaluate side-chains 314 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 265 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 315 PHE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 406 MET Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 460 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 20.0000 chunk 34 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 254 optimal weight: 20.0000 chunk 168 optimal weight: 20.0000 chunk 300 optimal weight: 0.7980 chunk 188 optimal weight: 8.9990 chunk 183 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN G 327 HIS ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 HIS H 45 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 26104 Z= 0.428 Angle : 0.627 12.076 35504 Z= 0.309 Chirality : 0.046 0.432 3900 Planarity : 0.006 0.049 4432 Dihedral : 8.499 59.185 3797 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.36 % Allowed : 16.26 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.15), residues: 3076 helix: 0.79 (0.12), residues: 1980 sheet: -1.01 (0.46), residues: 112 loop : -0.35 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 106 HIS 0.007 0.002 HIS G 77 PHE 0.021 0.002 PHE A 198 TYR 0.017 0.002 TYR D 70 ARG 0.004 0.000 ARG C 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 277 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7928 (ptt180) cc_final: 0.6663 (tpp80) REVERT: A 53 ASP cc_start: 0.7441 (t70) cc_final: 0.7169 (t0) REVERT: A 190 ARG cc_start: 0.5681 (ttt90) cc_final: 0.4930 (tmm160) REVERT: A 194 PHE cc_start: 0.7263 (m-80) cc_final: 0.6893 (m-10) REVERT: A 199 PHE cc_start: 0.7636 (m-80) cc_final: 0.7353 (m-10) REVERT: C 9 ARG cc_start: 0.7914 (ptt180) cc_final: 0.6666 (mtt180) REVERT: C 41 ASP cc_start: 0.5858 (t0) cc_final: 0.5512 (p0) REVERT: C 53 ASP cc_start: 0.7387 (t70) cc_final: 0.7125 (t0) REVERT: C 190 ARG cc_start: 0.5543 (ttt90) cc_final: 0.4692 (tmm160) REVERT: C 199 PHE cc_start: 0.7713 (m-80) cc_final: 0.7221 (m-10) REVERT: C 406 MET cc_start: 0.8836 (ptp) cc_final: 0.8569 (ptm) REVERT: B 9 ARG cc_start: 0.7934 (ptt180) cc_final: 0.6619 (tpp80) REVERT: B 45 HIS cc_start: 0.6499 (OUTLIER) cc_final: 0.6131 (t70) REVERT: B 53 ASP cc_start: 0.7450 (t70) cc_final: 0.7175 (t0) REVERT: B 190 ARG cc_start: 0.5498 (ttt90) cc_final: 0.4730 (tmm160) REVERT: B 199 PHE cc_start: 0.7648 (m-80) cc_final: 0.7216 (t80) REVERT: B 323 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8754 (ttpp) REVERT: B 422 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8046 (mm) REVERT: D 9 ARG cc_start: 0.7915 (ptt180) cc_final: 0.6623 (tpp80) REVERT: D 53 ASP cc_start: 0.7430 (t70) cc_final: 0.7149 (t0) REVERT: D 190 ARG cc_start: 0.5635 (ttt90) cc_final: 0.4544 (tmm160) REVERT: D 194 PHE cc_start: 0.7271 (m-80) cc_final: 0.6747 (m-10) REVERT: D 199 PHE cc_start: 0.7721 (m-80) cc_final: 0.7416 (m-80) REVERT: D 213 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7392 (mp0) REVERT: D 327 HIS cc_start: 0.8077 (m-70) cc_final: 0.7763 (m-70) REVERT: E 89 GLU cc_start: 0.6202 (tt0) cc_final: 0.5911 (tm-30) REVERT: E 321 ILE cc_start: 0.7463 (tp) cc_final: 0.7256 (tt) REVERT: E 449 LYS cc_start: 0.7227 (mmtt) cc_final: 0.6757 (ttpp) REVERT: G 197 LEU cc_start: 0.5721 (OUTLIER) cc_final: 0.5299 (tt) REVERT: H 45 HIS cc_start: 0.6377 (m-70) cc_final: 0.5796 (t70) REVERT: H 53 ASP cc_start: 0.6851 (t0) cc_final: 0.6491 (t0) REVERT: H 331 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7874 (mm) outliers start: 85 outliers final: 52 residues processed: 346 average time/residue: 0.4030 time to fit residues: 213.2570 Evaluate side-chains 320 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 263 time to evaluate : 3.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 323 LYS Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 451 LYS Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 406 MET Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Chi-restraints excluded: chain H residue 460 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 20.0000 chunk 120 optimal weight: 0.7980 chunk 179 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 chunk 204 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 236 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS E 220 ASN ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 26104 Z= 0.262 Angle : 0.572 16.443 35504 Z= 0.276 Chirality : 0.043 0.426 3900 Planarity : 0.005 0.046 4432 Dihedral : 8.316 59.336 3797 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.57 % Allowed : 17.17 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.15), residues: 3076 helix: 0.89 (0.12), residues: 1988 sheet: -0.98 (0.46), residues: 112 loop : -0.18 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 255 HIS 0.003 0.001 HIS G 45 PHE 0.033 0.001 PHE E 198 TYR 0.014 0.001 TYR G 365 ARG 0.003 0.000 ARG C 326 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 282 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7936 (ptt180) cc_final: 0.6683 (tpp80) REVERT: A 53 ASP cc_start: 0.7384 (t70) cc_final: 0.7023 (t0) REVERT: A 190 ARG cc_start: 0.5733 (ttt90) cc_final: 0.5018 (tmm160) REVERT: A 194 PHE cc_start: 0.7247 (m-80) cc_final: 0.6895 (m-10) REVERT: A 199 PHE cc_start: 0.7583 (m-80) cc_final: 0.7288 (m-10) REVERT: C 9 ARG cc_start: 0.7932 (ptt180) cc_final: 0.6663 (tpp80) REVERT: C 41 ASP cc_start: 0.5756 (t0) cc_final: 0.5353 (p0) REVERT: C 53 ASP cc_start: 0.7408 (t70) cc_final: 0.7153 (t0) REVERT: C 190 ARG cc_start: 0.5511 (ttt90) cc_final: 0.4641 (tmm160) REVERT: C 199 PHE cc_start: 0.7742 (m-80) cc_final: 0.7240 (m-10) REVERT: C 406 MET cc_start: 0.8688 (ptp) cc_final: 0.8412 (ptm) REVERT: B 9 ARG cc_start: 0.7972 (ptt180) cc_final: 0.6707 (tpp80) REVERT: B 45 HIS cc_start: 0.6512 (OUTLIER) cc_final: 0.6181 (t70) REVERT: B 53 ASP cc_start: 0.7397 (t70) cc_final: 0.7122 (t0) REVERT: B 190 ARG cc_start: 0.5565 (ttt90) cc_final: 0.4774 (tmm160) REVERT: B 199 PHE cc_start: 0.7376 (m-80) cc_final: 0.6880 (m-80) REVERT: B 255 TRP cc_start: 0.7933 (OUTLIER) cc_final: 0.7660 (t60) REVERT: B 458 LYS cc_start: 0.6286 (mtmt) cc_final: 0.5953 (mttm) REVERT: D 9 ARG cc_start: 0.7928 (ptt180) cc_final: 0.6687 (tpp80) REVERT: D 53 ASP cc_start: 0.7383 (t70) cc_final: 0.7082 (t0) REVERT: D 190 ARG cc_start: 0.5679 (ttt90) cc_final: 0.4664 (tmm160) REVERT: D 194 PHE cc_start: 0.7201 (m-80) cc_final: 0.6819 (m-10) REVERT: D 199 PHE cc_start: 0.7619 (m-80) cc_final: 0.7290 (m-80) REVERT: E 89 GLU cc_start: 0.6172 (tt0) cc_final: 0.5901 (tm-30) REVERT: E 321 ILE cc_start: 0.7476 (tp) cc_final: 0.7269 (tt) REVERT: E 449 LYS cc_start: 0.7234 (mmtt) cc_final: 0.6790 (ttpp) REVERT: F 323 LYS cc_start: 0.7380 (mmtm) cc_final: 0.6845 (mmtt) REVERT: H 53 ASP cc_start: 0.6772 (t0) cc_final: 0.6390 (t0) REVERT: H 331 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7861 (mm) outliers start: 65 outliers final: 45 residues processed: 334 average time/residue: 0.3889 time to fit residues: 200.2065 Evaluate side-chains 313 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 265 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 255 TRP Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 389 ILE Chi-restraints excluded: chain H residue 441 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.9990 chunk 288 optimal weight: 10.0000 chunk 262 optimal weight: 5.9990 chunk 280 optimal weight: 0.5980 chunk 168 optimal weight: 30.0000 chunk 122 optimal weight: 0.6980 chunk 220 optimal weight: 8.9990 chunk 85 optimal weight: 0.2980 chunk 253 optimal weight: 20.0000 chunk 265 optimal weight: 6.9990 chunk 279 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5916 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26104 Z= 0.175 Angle : 0.535 15.486 35504 Z= 0.256 Chirality : 0.041 0.423 3900 Planarity : 0.005 0.044 4432 Dihedral : 8.132 59.077 3797 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.14 % Allowed : 17.88 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.16), residues: 3076 helix: 1.04 (0.12), residues: 2012 sheet: -0.79 (0.47), residues: 112 loop : 0.03 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 255 HIS 0.003 0.001 HIS D 43 PHE 0.025 0.001 PHE E 194 TYR 0.012 0.001 TYR G 365 ARG 0.003 0.000 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 279 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7938 (ptt180) cc_final: 0.6696 (tpp80) REVERT: A 53 ASP cc_start: 0.7387 (t70) cc_final: 0.7126 (t0) REVERT: A 190 ARG cc_start: 0.5710 (ttt90) cc_final: 0.5022 (tmm160) REVERT: A 194 PHE cc_start: 0.7234 (m-80) cc_final: 0.6867 (m-10) REVERT: A 199 PHE cc_start: 0.7525 (m-80) cc_final: 0.7223 (m-10) REVERT: A 213 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7362 (mt-10) REVERT: C 9 ARG cc_start: 0.7923 (ptt180) cc_final: 0.6675 (tpp80) REVERT: C 53 ASP cc_start: 0.7399 (t70) cc_final: 0.7167 (t0) REVERT: C 190 ARG cc_start: 0.5502 (ttt90) cc_final: 0.4548 (tmm160) REVERT: C 199 PHE cc_start: 0.7649 (m-80) cc_final: 0.7132 (m-10) REVERT: B 9 ARG cc_start: 0.7959 (ptt180) cc_final: 0.6718 (tpp80) REVERT: B 45 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.6090 (t70) REVERT: B 53 ASP cc_start: 0.7443 (t70) cc_final: 0.7177 (t0) REVERT: B 106 TRP cc_start: 0.7791 (t-100) cc_final: 0.7546 (t-100) REVERT: B 190 ARG cc_start: 0.5492 (ttt90) cc_final: 0.4697 (tmm160) REVERT: B 458 LYS cc_start: 0.6321 (mtmt) cc_final: 0.5975 (mttm) REVERT: D 9 ARG cc_start: 0.7913 (ptt180) cc_final: 0.6693 (tpp80) REVERT: D 53 ASP cc_start: 0.7414 (t70) cc_final: 0.7141 (t0) REVERT: D 190 ARG cc_start: 0.5632 (ttt90) cc_final: 0.4561 (tmm160) REVERT: D 194 PHE cc_start: 0.7158 (m-80) cc_final: 0.6620 (m-10) REVERT: D 199 PHE cc_start: 0.7627 (m-80) cc_final: 0.6885 (m-80) REVERT: D 255 TRP cc_start: 0.7967 (t60) cc_final: 0.7119 (t60) REVERT: E 89 GLU cc_start: 0.6202 (tt0) cc_final: 0.5922 (tm-30) REVERT: E 321 ILE cc_start: 0.7373 (tp) cc_final: 0.7141 (tt) REVERT: E 449 LYS cc_start: 0.7214 (mmtt) cc_final: 0.6739 (ttpp) outliers start: 54 outliers final: 37 residues processed: 318 average time/residue: 0.3928 time to fit residues: 190.9959 Evaluate side-chains 306 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 441 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 10.0000 chunk 296 optimal weight: 30.0000 chunk 180 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 205 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 chunk 247 optimal weight: 0.0470 chunk 25 optimal weight: 0.7980 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN E 220 ASN ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26104 Z= 0.327 Angle : 0.605 14.549 35504 Z= 0.294 Chirality : 0.044 0.428 3900 Planarity : 0.005 0.048 4432 Dihedral : 8.247 58.606 3796 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.02 % Allowed : 17.80 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.16), residues: 3076 helix: 0.87 (0.12), residues: 2012 sheet: -0.82 (0.48), residues: 112 loop : -0.05 (0.21), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 392 HIS 0.004 0.001 HIS G 77 PHE 0.019 0.001 PHE E 315 TYR 0.012 0.001 TYR D 70 ARG 0.003 0.000 ARG D 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6152 Ramachandran restraints generated. 3076 Oldfield, 0 Emsley, 3076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 269 time to evaluate : 2.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ARG cc_start: 0.7934 (ptt180) cc_final: 0.6657 (tpp80) REVERT: A 53 ASP cc_start: 0.7387 (t70) cc_final: 0.7118 (t0) REVERT: A 190 ARG cc_start: 0.5808 (ttt90) cc_final: 0.5121 (tmm160) REVERT: A 194 PHE cc_start: 0.7225 (m-80) cc_final: 0.6870 (m-10) REVERT: A 199 PHE cc_start: 0.7570 (m-80) cc_final: 0.7254 (m-10) REVERT: A 213 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7389 (mt-10) REVERT: C 9 ARG cc_start: 0.7893 (ptt180) cc_final: 0.6581 (tpp80) REVERT: C 41 ASP cc_start: 0.5563 (t0) cc_final: 0.4906 (p0) REVERT: C 53 ASP cc_start: 0.7435 (t70) cc_final: 0.7185 (t0) REVERT: C 190 ARG cc_start: 0.5548 (ttt90) cc_final: 0.4584 (tmm160) REVERT: C 199 PHE cc_start: 0.7714 (m-80) cc_final: 0.7061 (m-10) REVERT: B 9 ARG cc_start: 0.7900 (ptt180) cc_final: 0.6583 (tpp80) REVERT: B 45 HIS cc_start: 0.6540 (OUTLIER) cc_final: 0.6148 (t70) REVERT: B 53 ASP cc_start: 0.7409 (t70) cc_final: 0.7139 (t0) REVERT: B 190 ARG cc_start: 0.5562 (ttt90) cc_final: 0.4745 (tmm160) REVERT: B 199 PHE cc_start: 0.7631 (m-80) cc_final: 0.7073 (m-10) REVERT: B 255 TRP cc_start: 0.8219 (t60) cc_final: 0.7883 (t60) REVERT: B 458 LYS cc_start: 0.6385 (mtmt) cc_final: 0.6029 (mttm) REVERT: D 9 ARG cc_start: 0.7878 (ptt180) cc_final: 0.6578 (tpp80) REVERT: D 53 ASP cc_start: 0.7411 (t70) cc_final: 0.7121 (t0) REVERT: D 190 ARG cc_start: 0.5735 (ttt90) cc_final: 0.4758 (tmm160) REVERT: D 194 PHE cc_start: 0.7262 (m-80) cc_final: 0.6876 (m-10) REVERT: D 199 PHE cc_start: 0.7652 (m-80) cc_final: 0.6854 (m-80) REVERT: D 255 TRP cc_start: 0.7984 (t60) cc_final: 0.7086 (t60) REVERT: E 89 GLU cc_start: 0.6169 (tt0) cc_final: 0.5899 (tm-30) REVERT: E 321 ILE cc_start: 0.7427 (tp) cc_final: 0.7143 (tt) REVERT: E 449 LYS cc_start: 0.7247 (mmtt) cc_final: 0.6776 (ttpp) REVERT: H 398 MET cc_start: 0.7321 (tpt) cc_final: 0.7067 (tpp) outliers start: 51 outliers final: 41 residues processed: 312 average time/residue: 0.3978 time to fit residues: 190.5432 Evaluate side-chains 307 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 265 time to evaluate : 2.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 375 ASP Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 45 HIS Chi-restraints excluded: chain E residue 252 CYS Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 441 MET Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 252 CYS Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 441 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 45 HIS Chi-restraints excluded: chain F residue 252 CYS Chi-restraints excluded: chain F residue 365 TYR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 441 MET Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 252 CYS Chi-restraints excluded: chain H residue 441 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.7980 chunk 263 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 36 optimal weight: 0.0000 chunk 68 optimal weight: 2.9990 chunk 247 optimal weight: 20.0000 chunk 103 optimal weight: 6.9990 chunk 254 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 450 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.199643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.160686 restraints weight = 35567.963| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.66 r_work: 0.3650 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26104 Z= 0.196 Angle : 0.547 14.261 35504 Z= 0.263 Chirality : 0.041 0.412 3900 Planarity : 0.005 0.046 4432 Dihedral : 8.148 59.756 3796 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.70 % Allowed : 18.20 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.16), residues: 3076 helix: 1.01 (0.12), residues: 2008 sheet: -0.78 (0.48), residues: 112 loop : 0.07 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 392 HIS 0.002 0.001 HIS C 43 PHE 0.019 0.001 PHE E 315 TYR 0.012 0.001 TYR G 365 ARG 0.004 0.000 ARG D 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5863.45 seconds wall clock time: 106 minutes 49.11 seconds (6409.11 seconds total)