Starting phenix.real_space_refine (version: dev) on Sat Feb 25 13:08:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2023/7phk_13418_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2023/7phk_13418.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2023/7phk_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_2023/7phk_13418_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2023/7phk_13418_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2023/7phk_13418.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2023/7phk_13418.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2023/7phk_13418_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7phk_13418/02_2023/7phk_13418_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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 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-4877/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: 14.12, per 1000 atoms: 0.56 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: 11.51 Conformation dependent library (CDL) restraints added in 4.2 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: 2.61 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: 7.95 Time building geometry restraints manager: 12.19 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: 823 33.92 - 50.89: 210 50.89 - 67.85: 97 67.85 - 84.81: 40 Dihedral angle restraints: 15128 sinusoidal: 5964 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 15125 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 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. 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: 4.960 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: 0.030 Extract box with map and model: 21.330 Check model and map are aligned: 0.400 Process input model: 70.700 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.260 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 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 : 13.694 84.811 9184 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 % 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 *********************** 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 : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 12 residues processed: 574 average time/residue: 0.4157 time to fit residues: 353.1074 Evaluate side-chains 310 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 298 time to evaluate : 2.931 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2227 time to fit residues: 9.3397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 159 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 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: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS A 450 GLN 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 26104 Z= 0.334 Angle : 0.604 11.564 35504 Z= 0.297 Chirality : 0.044 0.186 3900 Planarity : 0.005 0.049 4432 Dihedral : 9.455 61.387 3764 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer Outliers : 2.22 % 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: 0.49 (0.15), residues: 3076 helix: 1.03 (0.12), residues: 1900 sheet: -0.59 (0.55), residues: 88 loop : -0.76 (0.18), residues: 1088 *********************** 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 384 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 328 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 32 residues processed: 371 average time/residue: 0.4012 time to fit residues: 226.9501 Evaluate side-chains 311 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 3.016 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2404 time to fit residues: 18.2219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 235 optimal weight: 0.5980 chunk 192 optimal weight: 0.7980 chunk 78 optimal weight: 0.3980 chunk 283 optimal weight: 0.6980 chunk 306 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 chunk 281 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 GLN C 22 HIS C 327 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 HIS H 381 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.2774 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= 0.175 Angle : 0.521 9.891 35504 Z= 0.250 Chirality : 0.041 0.324 3900 Planarity : 0.004 0.042 4432 Dihedral : 8.715 61.974 3764 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.50 % 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: 0.98 (0.15), residues: 3076 helix: 1.27 (0.12), residues: 1952 sheet: 0.58 (1.05), residues: 32 loop : -0.37 (0.18), residues: 1092 *********************** 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 351 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 313 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 19 residues processed: 342 average time/residue: 0.3958 time to fit residues: 208.3067 Evaluate side-chains 289 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 270 time to evaluate : 2.966 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2362 time to fit residues: 12.6426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.9990 chunk 213 optimal weight: 20.0000 chunk 147 optimal weight: 0.7980 chunk 31 optimal weight: 0.0570 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 20.0000 chunk 284 optimal weight: 0.5980 chunk 301 optimal weight: 8.9990 chunk 148 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN D 22 HIS ** D 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 ASN ** E 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 26104 Z= 0.166 Angle : 0.513 10.988 35504 Z= 0.246 Chirality : 0.041 0.368 3900 Planarity : 0.004 0.041 4432 Dihedral : 8.176 61.759 3764 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.87 % 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: 1.23 (0.15), residues: 3076 helix: 1.40 (0.12), residues: 1948 sheet: 0.91 (1.11), residues: 32 loop : -0.12 (0.19), residues: 1096 *********************** 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 323 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 301 time to evaluate : 3.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 6 residues processed: 313 average time/residue: 0.3942 time to fit residues: 192.6655 Evaluate side-chains 272 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 266 time to evaluate : 2.992 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2311 time to fit residues: 6.8395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 0.3980 chunk 171 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 224 optimal weight: 20.0000 chunk 124 optimal weight: 0.5980 chunk 257 optimal weight: 7.9990 chunk 208 optimal weight: 20.0000 chunk 0 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 383 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 HIS D 450 GLN E 220 ASN E 336 HIS ** E 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6259 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 26104 Z= 0.332 Angle : 0.591 11.618 35504 Z= 0.290 Chirality : 0.044 0.382 3900 Planarity : 0.005 0.046 4432 Dihedral : 8.115 63.885 3764 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 1.62 % 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: 0.96 (0.15), residues: 3076 helix: 1.16 (0.12), residues: 1968 sheet: 0.06 (0.62), residues: 72 loop : -0.18 (0.19), residues: 1036 *********************** 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 320 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 279 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 17 residues processed: 306 average time/residue: 0.4110 time to fit residues: 196.3151 Evaluate side-chains 268 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 251 time to evaluate : 2.706 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2240 time to fit residues: 11.0346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 2.9990 chunk 271 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 301 optimal weight: 10.0000 chunk 250 optimal weight: 0.3980 chunk 139 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 HIS E 220 ASN E 381 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: 0.6246 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 26104 Z= 0.274 Angle : 0.551 11.470 35504 Z= 0.270 Chirality : 0.042 0.354 3900 Planarity : 0.005 0.045 4432 Dihedral : 7.949 63.127 3764 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.15), residues: 3076 helix: 1.27 (0.12), residues: 1924 sheet: 0.59 (1.08), residues: 32 loop : -0.12 (0.18), residues: 1120 *********************** 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 307 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 276 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 14 residues processed: 298 average time/residue: 0.4103 time to fit residues: 189.7316 Evaluate side-chains 275 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 261 time to evaluate : 2.917 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2457 time to fit residues: 10.3754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 171 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 300 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 138 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN ** C 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN D 327 HIS D 438 ASN D 450 GLN E 45 HIS E 220 ASN G 45 HIS G 336 HIS ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 HIS H 336 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.092 26104 Z= 0.709 Angle : 0.766 15.196 35504 Z= 0.384 Chirality : 0.052 0.409 3900 Planarity : 0.007 0.070 4432 Dihedral : 8.615 63.222 3764 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.74 % 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: 0.36 (0.15), residues: 3076 helix: 0.73 (0.12), residues: 1892 sheet: -0.66 (0.46), residues: 112 loop : -0.37 (0.19), residues: 1072 *********************** 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 321 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 277 time to evaluate : 3.858 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 313 average time/residue: 0.3999 time to fit residues: 193.6286 Evaluate side-chains 278 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 257 time to evaluate : 2.891 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2250 time to fit residues: 12.8977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 30.0000 chunk 120 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 236 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN C 438 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN D 438 ASN E 220 ASN ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.4094 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= 0.194 Angle : 0.542 12.538 35504 Z= 0.265 Chirality : 0.040 0.398 3900 Planarity : 0.005 0.042 4432 Dihedral : 8.159 59.593 3764 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.71 % 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: 0.81 (0.15), residues: 3076 helix: 1.06 (0.12), residues: 1920 sheet: -0.59 (0.58), residues: 72 loop : -0.18 (0.19), residues: 1084 *********************** 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 297 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 279 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 3 residues processed: 292 average time/residue: 0.4161 time to fit residues: 187.1607 Evaluate side-chains 256 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 253 time to evaluate : 2.962 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2098 time to fit residues: 5.0496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 1.9990 chunk 288 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 chunk 168 optimal weight: 30.0000 chunk 122 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 GLN E 220 ASN G 327 HIS ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.4221 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= 0.280 Angle : 0.573 11.746 35504 Z= 0.282 Chirality : 0.042 0.398 3900 Planarity : 0.005 0.044 4432 Dihedral : 7.977 59.288 3764 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.44 % 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: 0.70 (0.15), residues: 3076 helix: 0.93 (0.12), residues: 1952 sheet: -0.48 (0.45), residues: 112 loop : -0.14 (0.20), residues: 1012 *********************** 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 263 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 252 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 260 average time/residue: 0.4099 time to fit residues: 164.3431 Evaluate side-chains 247 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 3.142 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2391 time to fit residues: 5.5433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 6.9990 chunk 296 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 140 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 310 optimal weight: 4.9990 chunk 286 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN ** C 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN D 438 ASN E 220 ASN ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.098 26104 Z= 0.772 Angle : 0.810 27.414 35504 Z= 0.406 Chirality : 0.054 0.430 3900 Planarity : 0.007 0.074 4432 Dihedral : 8.672 58.728 3764 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 0.75 % 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: -0.00 (0.15), residues: 3076 helix: 0.39 (0.12), residues: 1936 sheet: -0.57 (0.46), residues: 112 loop : -0.45 (0.20), residues: 1028 ********************** 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 273 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 254 time to evaluate : 3.028 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 267 average time/residue: 0.4193 time to fit residues: 173.5935 Evaluate side-chains 248 residues out of total 2724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 240 time to evaluate : 3.034 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2393 time to fit residues: 7.7729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.9990 chunk 263 optimal weight: 8.9990 chunk 75 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 247 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 254 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 ASN ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 ASN E 220 ASN ** G 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.198862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.160439 restraints weight = 35546.327| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.61 r_work: 0.3710 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 26104 Z= 0.186 Angle : 0.553 11.649 35504 Z= 0.271 Chirality : 0.041 0.396 3900 Planarity : 0.005 0.044 4432 Dihedral : 8.094 59.502 3764 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 0.12 % 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: 0.42 (0.15), residues: 3076 helix: 0.69 (0.12), residues: 1988 sheet: -0.64 (0.59), residues: 72 loop : -0.27 (0.20), residues: 1016 =============================================================================== Job complete usr+sys time: 5454.23 seconds wall clock time: 100 minutes 12.01 seconds (6012.01 seconds total)