Starting phenix.real_space_refine on Tue Feb 20 18:19:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybs_10772/02_2024/6ybs_10772_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybs_10772/02_2024/6ybs_10772.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybs_10772/02_2024/6ybs_10772_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/6ybs_10772/02_2024/6ybs_10772_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybs_10772/02_2024/6ybs_10772_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybs_10772/02_2024/6ybs_10772.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybs_10772/02_2024/6ybs_10772.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybs_10772/02_2024/6ybs_10772_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ybs_10772/02_2024/6ybs_10772_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 501 5.49 5 Mg 29 5.21 5 S 85 5.16 5 C 16104 2.51 5 N 5248 2.21 5 O 6764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "x GLU 294": "OE1" <-> "OE2" Residue "x GLU 298": "OE1" <-> "OE2" Residue "x GLU 303": "OE1" <-> "OE2" Residue "x GLU 316": "OE1" <-> "OE2" Residue "x ARG 330": "NH1" <-> "NH2" Residue "x GLU 353": "OE1" <-> "OE2" Residue "x ARG 363": "NH1" <-> "NH2" Residue "x GLU 377": "OE1" <-> "OE2" Residue "x GLU 399": "OE1" <-> "OE2" Residue "x GLU 425": "OE1" <-> "OE2" Residue "x ARG 463": "NH1" <-> "NH2" Residue "x GLU 476": "OE1" <-> "OE2" Residue "c GLU 3": "OE1" <-> "OE2" Residue "c ARG 47": "NH1" <-> "NH2" Residue "c GLU 49": "OE1" <-> "OE2" Residue "c ARG 57": "NH1" <-> "NH2" Residue "c ARG 100": "NH1" <-> "NH2" Residue "c ASP 126": "OD1" <-> "OD2" Residue "c ASP 144": "OD1" <-> "OD2" Residue "c GLU 149": "OE1" <-> "OE2" Residue "c ASP 171": "OD1" <-> "OD2" Residue "c GLU 223": "OE1" <-> "OE2" Residue "c ASP 234": "OD1" <-> "OD2" Residue "c GLU 262": "OE1" <-> "OE2" Residue "c GLU 269": "OE1" <-> "OE2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n ARG 40": "NH1" <-> "NH2" Residue "n ARG 44": "NH1" <-> "NH2" Residue "n GLU 52": "OE1" <-> "OE2" Residue "n GLU 60": "OE1" <-> "OE2" Residue "n GLU 62": "OE1" <-> "OE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 5": "NH1" <-> "NH2" Residue "h ARG 21": "NH1" <-> "NH2" Residue "h PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 87": "NH1" <-> "NH2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "h GLU 107": "OE1" <-> "OE2" Residue "h GLU 111": "OE1" <-> "OE2" Residue "o GLU 248": "OE1" <-> "OE2" Residue "o ASP 249": "OD1" <-> "OD2" Residue "o GLU 252": "OE1" <-> "OE2" Residue "o GLU 257": "OE1" <-> "OE2" Residue "o ARG 295": "NH1" <-> "NH2" Residue "o ASP 306": "OD1" <-> "OD2" Residue "o GLU 313": "OE1" <-> "OE2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 74": "OE1" <-> "OE2" Residue "m ASP 29": "OD1" <-> "OD2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m GLU 71": "OE1" <-> "OE2" Residue "m ASP 81": "OD1" <-> "OD2" Residue "m ASP 122": "OD1" <-> "OD2" Residue "m GLU 125": "OE1" <-> "OE2" Residue "m GLU 126": "OE1" <-> "OE2" Residue "b GLU 31": "OE1" <-> "OE2" Residue "b ARG 61": "NH1" <-> "NH2" Residue "b GLU 66": "OE1" <-> "OE2" Residue "b GLU 71": "OE1" <-> "OE2" Residue "b GLU 110": "OE1" <-> "OE2" Residue "Z ARG 9": "NH1" <-> "NH2" Residue "Z GLU 20": "OE1" <-> "OE2" Residue "Z GLU 31": "OE1" <-> "OE2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z GLU 47": "OE1" <-> "OE2" Residue "Z GLU 61": "OE1" <-> "OE2" Residue "Z GLU 81": "OE1" <-> "OE2" Residue "Z GLU 85": "OE1" <-> "OE2" Residue "Z ARG 94": "NH1" <-> "NH2" Residue "Z ARG 143": "NH1" <-> "NH2" Residue "Z ASP 154": "OD1" <-> "OD2" Residue "Z ASP 169": "OD1" <-> "OD2" Residue "Z GLU 216": "OE1" <-> "OE2" Residue "d GLU 13": "OE1" <-> "OE2" Residue "d GLU 44": "OE1" <-> "OE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "d ARG 62": "NH1" <-> "NH2" Residue "d ARG 102": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "e GLU 75": "OE1" <-> "OE2" Residue "e ARG 80": "NH1" <-> "NH2" Residue "f ARG 14": "NH1" <-> "NH2" Residue "f ARG 39": "NH1" <-> "NH2" Residue "f ASP 49": "OD1" <-> "OD2" Residue "f ARG 55": "NH1" <-> "NH2" Residue "f GLU 61": "OE1" <-> "OE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "f ASP 81": "OD1" <-> "OD2" Residue "f ARG 86": "NH1" <-> "NH2" Residue "f ARG 108": "NH1" <-> "NH2" Residue "f ARG 141": "NH1" <-> "NH2" Residue "f ARG 142": "NH1" <-> "NH2" Residue "V ASP 32": "OD1" <-> "OD2" Residue "V ASP 37": "OD1" <-> "OD2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V ARG 71": "NH1" <-> "NH2" Residue "V ARG 81": "NH1" <-> "NH2" Residue "V ARG 127": "NH1" <-> "NH2" Residue "V ARG 135": "NH1" <-> "NH2" Residue "V ARG 164": "NH1" <-> "NH2" Residue "V GLU 176": "OE1" <-> "OE2" Residue "k ARG 118": "NH1" <-> "NH2" Residue "Y GLU 43": "OE1" <-> "OE2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 62": "NH1" <-> "NH2" Residue "Y TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 101": "OD1" <-> "OD2" Residue "Y ARG 125": "NH1" <-> "NH2" Residue "Y ARG 126": "NH1" <-> "NH2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Y ARG 140": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28732 Number of models: 1 Model: "" Number of chains: 21 Chain: "x" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2317 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 13, 'TRANS': 346} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 633 Unresolved non-hydrogen angles: 806 Unresolved non-hydrogen dihedrals: 531 Unresolved non-hydrogen chiralities: 51 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 13, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 352 Chain: "c" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "n" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 498 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "X" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 641 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "h" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 817 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "o" Number of atoms: 616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 616 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "a" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 834 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 8, 'TRANS': 90} Chain: "m" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "i" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 419 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "b" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 913 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "Z" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1765 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 11, 'TRANS': 215} Chain: "d" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1105 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain: "e" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 523 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "f" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1176 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 3, 'TRANS': 138} Chain: "V" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "k" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 435 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain breaks: 1 Chain: "Y" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1124 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "A" Number of atoms: 10672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 10672 Classifications: {'RNA': 501} Modifications used: {'rna2p_pur': 45, 'rna2p_pyr': 44, 'rna3p': 3, 'rna3p_pur': 206, 'rna3p_pyr': 202} Link IDs: {'rna2p': 88, 'rna3p': 412} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 1 Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Unusual residues: {' MG': 28} Classifications: {'undetermined': 28} Link IDs: {None: 27} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16675 SG CYS k 121 93.746 165.640 39.991 1.00104.69 S ATOM 16711 SG CYS k 126 90.181 164.946 40.787 1.00109.17 S ATOM 16829 SG CYS k 141 93.957 165.708 43.630 1.00 95.97 S ATOM 16848 SG CYS k 144 94.487 162.654 41.866 1.00 99.65 S Time building chain proxies: 15.93, per 1000 atoms: 0.55 Number of scatterers: 28732 At special positions: 0 Unit cell: (148.212, 207.282, 131.028, 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 1 29.99 S 85 16.00 P 501 15.00 Mg 29 11.99 O 6764 8.00 N 5248 7.00 C 16104 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: 13.86 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN k 201 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 121 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 141 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 144 " pdb="ZN ZN k 201 " - pdb=" SG CYS k 126 " Number of angles added : 6 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 26 sheets defined 30.5% alpha, 15.5% beta 142 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 14.43 Creating SS restraints... Processing helix chain 'x' and resid 177 through 182 removed outlier: 3.700A pdb=" N LYS x 182 " --> pdb=" O PRO x 178 " (cutoff:3.500A) Processing helix chain 'x' and resid 205 through 208 No H-bonds generated for 'chain 'x' and resid 205 through 208' Processing helix chain 'x' and resid 234 through 237 No H-bonds generated for 'chain 'x' and resid 234 through 237' Processing helix chain 'x' and resid 254 through 257 No H-bonds generated for 'chain 'x' and resid 254 through 257' Processing helix chain 'x' and resid 310 through 326 removed outlier: 4.117A pdb=" N SER x 325 " --> pdb=" O ASN x 321 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN x 326 " --> pdb=" O HIS x 322 " (cutoff:3.500A) Processing helix chain 'x' and resid 418 through 428 Processing helix chain 'x' and resid 431 through 442 removed outlier: 3.677A pdb=" N CYS x 439 " --> pdb=" O ARG x 435 " (cutoff:3.500A) Processing helix chain 'x' and resid 476 through 480 Processing helix chain 'x' and resid 485 through 498 Processing helix chain 'X' and resid 7 through 23 removed outlier: 7.218A pdb=" N THR X 22 " --> pdb=" O GLU X 18 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG X 23 " --> pdb=" O LYS X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 38 Processing helix chain 'X' and resid 45 through 63 removed outlier: 3.702A pdb=" N ARG X 60 " --> pdb=" O HIS X 56 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN X 62 " --> pdb=" O MET X 58 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ARG X 63 " --> pdb=" O LYS X 59 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 74 No H-bonds generated for 'chain 'X' and resid 72 through 74' Processing helix chain 'h' and resid 29 through 45 Processing helix chain 'h' and resid 95 through 101 removed outlier: 3.710A pdb=" N GLN h 100 " --> pdb=" O GLU h 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 252 through 262 Proline residue: o 261 - end of helix Processing helix chain 'o' and resid 292 through 296 Processing helix chain 'o' and resid 305 through 307 No H-bonds generated for 'chain 'o' and resid 305 through 307' Processing helix chain 'a' and resid 5 through 18 Processing helix chain 'a' and resid 36 through 38 No H-bonds generated for 'chain 'a' and resid 36 through 38' Processing helix chain 'a' and resid 42 through 53 Processing helix chain 'a' and resid 73 through 82 removed outlier: 3.867A pdb=" N GLN a 77 " --> pdb=" O ASN a 73 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 27 Processing helix chain 'm' and resid 36 through 43 Processing helix chain 'm' and resid 59 through 72 removed outlier: 3.837A pdb=" N HIS m 72 " --> pdb=" O LEU m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 82 through 89 Processing helix chain 'm' and resid 120 through 131 removed outlier: 3.847A pdb=" N VAL m 123 " --> pdb=" O ALA m 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 33 through 35 No H-bonds generated for 'chain 'i' and resid 33 through 35' Processing helix chain 'i' and resid 40 through 50 removed outlier: 5.952A pdb=" N LYS i 48 " --> pdb=" O ARG i 44 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASP i 49 " --> pdb=" O GLN i 45 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 27 Processing helix chain 'b' and resid 30 through 36 removed outlier: 3.925A pdb=" N GLN b 35 " --> pdb=" O GLU b 31 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU b 36 " --> pdb=" O GLN b 32 " (cutoff:3.500A) Processing helix chain 'b' and resid 39 through 46 Processing helix chain 'b' and resid 51 through 64 Processing helix chain 'b' and resid 109 through 111 No H-bonds generated for 'chain 'b' and resid 109 through 111' Processing helix chain 'b' and resid 117 through 119 No H-bonds generated for 'chain 'b' and resid 117 through 119' Processing helix chain 'Z' and resid 7 through 28 Processing helix chain 'Z' and resid 30 through 32 No H-bonds generated for 'chain 'Z' and resid 30 through 32' Processing helix chain 'Z' and resid 55 through 59 Processing helix chain 'Z' and resid 64 through 77 Processing helix chain 'Z' and resid 98 through 110 Processing helix chain 'Z' and resid 115 through 129 Processing helix chain 'Z' and resid 163 through 165 No H-bonds generated for 'chain 'Z' and resid 163 through 165' Processing helix chain 'd' and resid 6 through 8 No H-bonds generated for 'chain 'd' and resid 6 through 8' Processing helix chain 'd' and resid 11 through 24 removed outlier: 3.933A pdb=" N ARG d 16 " --> pdb=" O GLN d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 34 through 36 No H-bonds generated for 'chain 'd' and resid 34 through 36' Processing helix chain 'd' and resid 52 through 65 Processing helix chain 'd' and resid 72 through 78 Processing helix chain 'd' and resid 97 through 109 Processing helix chain 'd' and resid 125 through 142 Processing helix chain 'e' and resid 52 through 64 removed outlier: 3.579A pdb=" N VAL e 62 " --> pdb=" O LEU e 58 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'e' and resid 73 through 76 No H-bonds generated for 'chain 'e' and resid 73 through 76' Processing helix chain 'e' and resid 81 through 94 Processing helix chain 'f' and resid 26 through 32 removed outlier: 3.612A pdb=" N ILE f 30 " --> pdb=" O ILE f 26 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA f 32 " --> pdb=" O PHE f 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 26 through 32' Processing helix chain 'f' and resid 38 through 47 Processing helix chain 'f' and resid 56 through 58 No H-bonds generated for 'chain 'f' and resid 56 through 58' Processing helix chain 'f' and resid 61 through 72 Processing helix chain 'f' and resid 75 through 77 No H-bonds generated for 'chain 'f' and resid 75 through 77' Processing helix chain 'f' and resid 81 through 83 No H-bonds generated for 'chain 'f' and resid 81 through 83' Processing helix chain 'f' and resid 102 through 116 Processing helix chain 'f' and resid 120 through 127 Processing helix chain 'V' and resid 19 through 21 No H-bonds generated for 'chain 'V' and resid 19 through 21' Processing helix chain 'V' and resid 62 through 65 Processing helix chain 'V' and resid 68 through 76 removed outlier: 3.637A pdb=" N MET V 76 " --> pdb=" O LEU V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 103 Processing helix chain 'V' and resid 108 through 119 Processing helix chain 'V' and resid 143 through 161 Processing helix chain 'V' and resid 169 through 182 Processing helix chain 'V' and resid 188 through 202 Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Y' and resid 45 through 58 removed outlier: 3.923A pdb=" N GLN Y 48 " --> pdb=" O ARG Y 45 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR Y 49 " --> pdb=" O THR Y 46 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS Y 50 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) Proline residue: Y 54 - end of helix removed outlier: 3.974A pdb=" N LEU Y 58 " --> pdb=" O VAL Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 99 Processing helix chain 'Y' and resid 102 through 115 Processing helix chain 'Y' and resid 117 through 119 No H-bonds generated for 'chain 'Y' and resid 117 through 119' Processing sheet with id= A, first strand: chain 'x' and resid 195 through 197 Processing sheet with id= B, first strand: chain 'x' and resid 278 through 281 removed outlier: 3.796A pdb=" N PHE x 278 " --> pdb=" O GLN x 271 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'x' and resid 392 through 396 removed outlier: 7.072A pdb=" N TYR x 447 " --> pdb=" O ASN x 393 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N LYS x 395 " --> pdb=" O TYR x 447 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LYS x 449 " --> pdb=" O LYS x 395 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY x 468 " --> pdb=" O TYR x 452 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N SER x 454 " --> pdb=" O ILE x 466 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ILE x 466 " --> pdb=" O SER x 454 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'x' and resid 170 through 176 removed outlier: 3.968A pdb=" N LYS x 172 " --> pdb=" O VAL x 520 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N VAL x 520 " --> pdb=" O LYS x 172 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU x 174 " --> pdb=" O ILE x 518 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE x 518 " --> pdb=" O GLU x 174 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'c' and resid 18 through 22 removed outlier: 6.764A pdb=" N ALA c 34 " --> pdb=" O THR c 19 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE c 21 " --> pdb=" O LEU c 32 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU c 32 " --> pdb=" O ILE c 21 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LYS c 44 " --> pdb=" O PRO c 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'c' and resid 66 through 71 removed outlier: 6.611A pdb=" N GLY c 81 " --> pdb=" O SER c 67 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL c 69 " --> pdb=" O LEU c 79 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU c 79 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ILE c 71 " --> pdb=" O PHE c 77 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE c 77 " --> pdb=" O ILE c 71 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG c 99 " --> pdb=" O LEU c 89 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ASP c 91 " --> pdb=" O THR c 97 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR c 97 " --> pdb=" O ASP c 91 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'c' and resid 129 through 133 removed outlier: 3.589A pdb=" N LYS c 130 " --> pdb=" O SER c 122 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'c' and resid 151 through 155 removed outlier: 7.066A pdb=" N CYS c 168 " --> pdb=" O SER c 152 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N VAL c 154 " --> pdb=" O VAL c 166 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL c 166 " --> pdb=" O VAL c 154 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ASN c 178 " --> pdb=" O LEU c 184 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU c 184 " --> pdb=" O ASN c 178 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'c' and resid 195 through 200 removed outlier: 7.164A pdb=" N GLY c 210 " --> pdb=" O ASN c 196 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N VAL c 198 " --> pdb=" O ALA c 208 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA c 208 " --> pdb=" O VAL c 198 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL c 200 " --> pdb=" O LEU c 206 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU c 206 " --> pdb=" O VAL c 200 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLY c 211 " --> pdb=" O GLN c 215 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLN c 215 " --> pdb=" O GLY c 211 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR c 228 " --> pdb=" O LEU c 218 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP c 220 " --> pdb=" O HIS c 226 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N HIS c 226 " --> pdb=" O ASP c 220 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'c' and resid 239 through 241 removed outlier: 4.026A pdb=" N ASP c 268 " --> pdb=" O ILE c 258 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP c 260 " --> pdb=" O ILE c 266 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE c 266 " --> pdb=" O ASP c 260 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'c' and resid 288 through 291 removed outlier: 4.051A pdb=" N SER c 288 " --> pdb=" O GLY c 301 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY c 9 " --> pdb=" O VAL c 309 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLN c 311 " --> pdb=" O LEU c 7 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU c 7 " --> pdb=" O GLN c 311 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'n' and resid 55 through 58 removed outlier: 7.020A pdb=" N ARG n 31 " --> pdb=" O THR n 15 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL n 17 " --> pdb=" O GLN n 29 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N GLN n 29 " --> pdb=" O VAL n 17 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'h' and resid 85 through 93 removed outlier: 3.726A pdb=" N SER h 93 " --> pdb=" O HIS h 18 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS h 18 " --> pdb=" O SER h 93 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'h' and resid 59 through 66 Processing sheet with id= O, first strand: chain 'o' and resid 241 through 244 Processing sheet with id= P, first strand: chain 'a' and resid 20 through 24 Processing sheet with id= Q, first strand: chain 'm' and resid 31 through 33 removed outlier: 3.957A pdb=" N LEU m 49 " --> pdb=" O VAL m 111 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE m 77 " --> pdb=" O CYS m 50 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU m 52 " --> pdb=" O ILE m 77 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'b' and resid 76 through 78 Processing sheet with id= S, first strand: chain 'Z' and resid 84 through 90 removed outlier: 5.981A pdb=" N THR Z 46 " --> pdb=" O GLU Z 85 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TYR Z 87 " --> pdb=" O THR Z 46 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE Z 48 " --> pdb=" O TYR Z 87 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLU Z 89 " --> pdb=" O ILE Z 48 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ILE Z 50 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Z' and resid 148 through 155 removed outlier: 3.660A pdb=" N GLY Z 133 " --> pdb=" O MET Z 189 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'd' and resid 81 through 83 Processing sheet with id= V, first strand: chain 'd' and resid 113 through 115 Processing sheet with id= W, first strand: chain 'e' and resid 99 through 102 removed outlier: 6.727A pdb=" N ILE e 108 " --> pdb=" O VAL e 100 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'V' and resid 123 through 125 Processing sheet with id= Y, first strand: chain 'k' and resid 132 through 134 Processing sheet with id= Z, first strand: chain 'Y' and resid 9 through 16 removed outlier: 3.522A pdb=" N LYS Y 16 " --> pdb=" O ALA Y 19 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU Y 31 " --> pdb=" O ILE Y 68 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL Y 70 " --> pdb=" O LEU Y 31 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS Y 33 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL Y 72 " --> pdb=" O LYS Y 33 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 570 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 18.45 Time building geometry restraints manager: 14.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5421 1.33 - 1.45: 9596 1.45 - 1.57: 14104 1.57 - 1.69: 1002 1.69 - 1.82: 127 Bond restraints: 30250 Sorted by residual: bond pdb=" C2' A2M A1678 " pdb=" C1' A2M A1678 " ideal model delta sigma weight residual 1.305 1.524 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" O4' A2M A1678 " pdb=" C1' A2M A1678 " ideal model delta sigma weight residual 1.615 1.407 0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C5 5MC A1374 " pdb=" C6 5MC A1374 " ideal model delta sigma weight residual 1.494 1.339 0.155 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C2 5MC A1374 " pdb=" N3 5MC A1374 " ideal model delta sigma weight residual 1.493 1.352 0.141 2.00e-02 2.50e+03 4.97e+01 bond pdb=" C4' A2M A1678 " pdb=" O4' A2M A1678 " ideal model delta sigma weight residual 1.305 1.445 -0.140 2.00e-02 2.50e+03 4.91e+01 ... (remaining 30245 not shown) Histogram of bond angle deviations from ideal: 94.59 - 102.81: 955 102.81 - 111.02: 13686 111.02 - 119.23: 13368 119.23 - 127.44: 14139 127.44 - 135.66: 1128 Bond angle restraints: 43276 Sorted by residual: angle pdb=" C1' A2M A1678 " pdb=" N9 A2M A1678 " pdb=" C8 A2M A1678 " ideal model delta sigma weight residual 88.50 126.20 -37.70 3.00e+00 1.11e-01 1.58e+02 angle pdb=" N6 A2M A1678 " pdb=" C6 A2M A1678 " pdb=" N1 A2M A1678 " ideal model delta sigma weight residual 92.14 118.76 -26.62 3.00e+00 1.11e-01 7.87e+01 angle pdb=" C4' G A1600 " pdb=" C3' G A1600 " pdb=" O3' G A1600 " ideal model delta sigma weight residual 109.40 119.45 -10.05 1.50e+00 4.44e-01 4.49e+01 angle pdb=" C3' G A1600 " pdb=" O3' G A1600 " pdb=" P A A1601 " ideal model delta sigma weight residual 120.20 128.82 -8.62 1.50e+00 4.44e-01 3.30e+01 angle pdb=" CG1 ILE x 481 " pdb=" CB ILE x 481 " pdb=" CG2 ILE x 481 " ideal model delta sigma weight residual 110.70 94.59 16.11 3.00e+00 1.11e-01 2.88e+01 ... (remaining 43271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 17506 35.55 - 71.10: 1392 71.10 - 106.65: 168 106.65 - 142.21: 3 142.21 - 177.76: 4 Dihedral angle restraints: 19073 sinusoidal: 12351 harmonic: 6722 Sorted by residual: dihedral pdb=" O4' U A1314 " pdb=" C1' U A1314 " pdb=" N1 U A1314 " pdb=" C2 U A1314 " ideal model delta sinusoidal sigma weight residual 200.00 49.52 150.48 1 1.50e+01 4.44e-03 7.98e+01 dihedral pdb=" O4' C A1453 " pdb=" C1' C A1453 " pdb=" N1 C A1453 " pdb=" C2 C A1453 " ideal model delta sinusoidal sigma weight residual 200.00 78.80 121.20 1 1.50e+01 4.44e-03 6.48e+01 dihedral pdb=" O4' U A1578 " pdb=" C1' U A1578 " pdb=" N1 U A1578 " pdb=" C2 U A1578 " ideal model delta sinusoidal sigma weight residual 232.00 75.00 157.00 1 1.70e+01 3.46e-03 6.38e+01 ... (remaining 19070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4730 0.087 - 0.175: 489 0.175 - 0.262: 43 0.262 - 0.349: 7 0.349 - 0.436: 5 Chirality restraints: 5274 Sorted by residual: chirality pdb=" C2' A2M A1678 " pdb=" C3' A2M A1678 " pdb=" O2' A2M A1678 " pdb=" C1' A2M A1678 " both_signs ideal model delta sigma weight residual False -2.39 -2.83 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" C3' G A1600 " pdb=" C4' G A1600 " pdb=" O3' G A1600 " pdb=" C2' G A1600 " both_signs ideal model delta sigma weight residual False -2.74 -2.34 -0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" C4' U A1242 " pdb=" C5' U A1242 " pdb=" O4' U A1242 " pdb=" C3' U A1242 " both_signs ideal model delta sigma weight residual False -2.50 -2.12 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 5271 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1374 " -0.043 2.00e-02 2.50e+03 5.64e-01 7.15e+03 pdb=" C4' 5MC A1374 " -0.429 2.00e-02 2.50e+03 pdb=" O4' 5MC A1374 " -0.577 2.00e-02 2.50e+03 pdb=" C3' 5MC A1374 " 0.591 2.00e-02 2.50e+03 pdb=" O3' 5MC A1374 " 0.580 2.00e-02 2.50e+03 pdb=" C2' 5MC A1374 " 0.205 2.00e-02 2.50e+03 pdb=" O2' 5MC A1374 " -0.935 2.00e-02 2.50e+03 pdb=" C1' 5MC A1374 " -0.223 2.00e-02 2.50e+03 pdb=" N1 5MC A1374 " 0.831 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' JMH A1219 " -0.108 2.00e-02 2.50e+03 8.87e-02 1.97e+02 pdb=" N1 JMH A1219 " 0.023 2.00e-02 2.50e+03 pdb=" C2 JMH A1219 " -0.006 2.00e-02 2.50e+03 pdb=" O2 JMH A1219 " -0.047 2.00e-02 2.50e+03 pdb=" N3 JMH A1219 " 0.030 2.00e-02 2.50e+03 pdb=" C4 JMH A1219 " -0.037 2.00e-02 2.50e+03 pdb=" N4 JMH A1219 " -0.166 2.00e-02 2.50e+03 pdb=" C5 JMH A1219 " 0.064 2.00e-02 2.50e+03 pdb=" C6 JMH A1219 " 0.125 2.00e-02 2.50e+03 pdb=" C31 JMH A1219 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU f 103 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C LEU f 103 " -0.072 2.00e-02 2.50e+03 pdb=" O LEU f 103 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP f 104 " 0.024 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 504 2.61 - 3.19: 22017 3.19 - 3.76: 50170 3.76 - 4.33: 69444 4.33 - 4.90: 103038 Nonbonded interactions: 245173 Sorted by model distance: nonbonded pdb=" O6 G A1517 " pdb="MG MG A1909 " model vdw 2.044 2.170 nonbonded pdb=" O6 G A1387 " pdb="MG MG A1918 " model vdw 2.050 2.170 nonbonded pdb=" OP2 G A1385 " pdb="MG MG A1918 " model vdw 2.053 2.170 nonbonded pdb=" OP2 C A1262 " pdb="MG MG A1909 " model vdw 2.061 2.170 nonbonded pdb=" OP2 A A1217 " pdb="MG MG A1901 " model vdw 2.071 2.170 ... (remaining 245168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.770 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: 26.520 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 99.270 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.219 30250 Z= 0.432 Angle : 0.980 37.695 43276 Z= 0.526 Chirality : 0.056 0.436 5274 Planarity : 0.011 0.564 3668 Dihedral : 21.200 177.757 14731 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.92 % Allowed : 17.10 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.15), residues: 2292 helix: -0.96 (0.17), residues: 723 sheet: -1.56 (0.23), residues: 428 loop : -2.25 (0.15), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP i 8 HIS 0.016 0.001 HIS o 288 PHE 0.032 0.003 PHE m 128 TYR 0.034 0.002 TYR Z 107 ARG 0.011 0.001 ARG V 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 552 time to evaluate : 2.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 391 PHE cc_start: 0.4619 (m-80) cc_final: 0.4093 (m-10) REVERT: x 418 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7722 (ttm-80) REVERT: x 446 GLU cc_start: 0.8293 (tp30) cc_final: 0.7817 (tp30) REVERT: c 291 TRP cc_start: 0.8488 (m100) cc_final: 0.8156 (m100) REVERT: n 31 ARG cc_start: 0.8233 (ptm160) cc_final: 0.7763 (ttp80) REVERT: n 60 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7865 (tm-30) REVERT: h 19 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7108 (mpt90) REVERT: a 53 LYS cc_start: 0.9262 (tmmt) cc_final: 0.9059 (ttpp) REVERT: a 73 ASN cc_start: 0.9030 (m-40) cc_final: 0.8806 (m-40) REVERT: m 71 GLU cc_start: 0.8341 (tt0) cc_final: 0.7862 (tt0) REVERT: i 54 LYS cc_start: 0.8995 (ttmt) cc_final: 0.8752 (ttmt) REVERT: b 58 LYS cc_start: 0.8712 (mmmt) cc_final: 0.8460 (mttp) REVERT: b 64 LYS cc_start: 0.8453 (tttt) cc_final: 0.8099 (ttpp) REVERT: b 82 ASP cc_start: 0.8170 (p0) cc_final: 0.7913 (p0) REVERT: Z 40 ARG cc_start: 0.8036 (ttm170) cc_final: 0.7780 (ttp-170) REVERT: Z 193 ASP cc_start: 0.8049 (p0) cc_final: 0.7835 (p0) REVERT: d 29 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7468 (tptt) REVERT: e 66 LYS cc_start: 0.8939 (mttt) cc_final: 0.7725 (mmpt) REVERT: e 94 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8415 (mtmm) REVERT: f 83 PHE cc_start: 0.9342 (OUTLIER) cc_final: 0.8129 (t80) REVERT: V 36 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7876 (tp40) REVERT: V 65 GLN cc_start: 0.8462 (mp10) cc_final: 0.8262 (mm-40) REVERT: V 194 ASP cc_start: 0.7949 (m-30) cc_final: 0.7665 (m-30) REVERT: k 107 LYS cc_start: 0.6524 (pttt) cc_final: 0.5756 (ptmt) REVERT: k 114 ILE cc_start: 0.7073 (mp) cc_final: 0.6829 (mp) REVERT: k 144 CYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8267 (p) REVERT: Y 106 LYS cc_start: 0.8135 (tttt) cc_final: 0.7887 (ttpp) outliers start: 54 outliers final: 38 residues processed: 593 average time/residue: 0.4512 time to fit residues: 405.4213 Evaluate side-chains 542 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 502 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 369 ASP Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 467 LEU Chi-restraints excluded: chain x residue 472 PHE Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 10 THR Chi-restraints excluded: chain c residue 72 SER Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 275 ILE Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain a residue 51 SER Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 66 GLU Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 94 ILE Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain m residue 132 LYS Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 119 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 144 CYS Chi-restraints excluded: chain Y residue 51 LEU Chi-restraints excluded: chain Y residue 129 SER Chi-restraints excluded: chain Y residue 143 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 233 optimal weight: 1.9990 chunk 209 optimal weight: 0.0040 chunk 116 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 217 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 161 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 305 ASN x 312 ASN x 327 GLN x 406 ASN x 429 ASN c 51 ASN c 162 ASN X 31 ASN X 62 GLN h 92 HIS m 46 GLN i 16 GLN i 26 ASN i 45 GLN b 32 GLN b 41 GLN b 103 ASN b 114 HIS Z 145 GLN d 85 ASN e 46 ASN e 106 GLN f 72 GLN f 76 GLN f 105 ASN V 31 ASN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 82 ASN V 148 ASN V 165 ASN V 179 ASN ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 11 GLN Y 35 ASN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30250 Z= 0.184 Angle : 0.575 15.601 43276 Z= 0.305 Chirality : 0.039 0.246 5274 Planarity : 0.005 0.124 3668 Dihedral : 21.627 160.344 10497 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.46 % Allowed : 19.81 % Favored : 76.73 % 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: -1.59 (0.16), residues: 2292 helix: 0.34 (0.19), residues: 725 sheet: -1.35 (0.23), residues: 433 loop : -1.87 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 177 HIS 0.004 0.001 HIS c 191 PHE 0.015 0.001 PHE a 67 TYR 0.033 0.001 TYR x 319 ARG 0.006 0.000 ARG k 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 506 time to evaluate : 2.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 371 ASP cc_start: 0.5022 (OUTLIER) cc_final: 0.4758 (t0) REVERT: x 391 PHE cc_start: 0.4617 (m-80) cc_final: 0.4110 (m-10) REVERT: x 418 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7491 (ttm-80) REVERT: x 446 GLU cc_start: 0.8138 (tp30) cc_final: 0.7792 (tp30) REVERT: c 113 PHE cc_start: 0.9190 (OUTLIER) cc_final: 0.8282 (t80) REVERT: n 31 ARG cc_start: 0.8288 (ptm160) cc_final: 0.7898 (ttm110) REVERT: n 60 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7791 (tm-30) REVERT: h 19 ARG cc_start: 0.7526 (mtp180) cc_final: 0.7177 (mpt90) REVERT: h 75 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8742 (mttp) REVERT: h 99 LYS cc_start: 0.8348 (mttm) cc_final: 0.7554 (mmtt) REVERT: o 306 ASP cc_start: 0.7654 (m-30) cc_final: 0.7405 (t0) REVERT: a 53 LYS cc_start: 0.9278 (tmmt) cc_final: 0.9056 (ttpp) REVERT: m 18 LEU cc_start: 0.9165 (tp) cc_final: 0.8919 (tp) REVERT: i 54 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8719 (ttmt) REVERT: i 56 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6531 (t0) REVERT: b 58 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8514 (mttp) REVERT: b 64 LYS cc_start: 0.8470 (tttt) cc_final: 0.8153 (ttpp) REVERT: Z 40 ARG cc_start: 0.8008 (ttm170) cc_final: 0.7693 (ttp-170) REVERT: Z 62 LYS cc_start: 0.8814 (ttmm) cc_final: 0.8597 (tttp) REVERT: Z 179 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6847 (tt0) REVERT: d 29 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7460 (tptt) REVERT: e 94 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8339 (mtmm) REVERT: f 83 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8102 (t80) REVERT: V 32 ASP cc_start: 0.8104 (t0) cc_final: 0.7782 (t0) REVERT: V 36 GLN cc_start: 0.8072 (tp-100) cc_final: 0.7697 (tp40) REVERT: V 37 ASP cc_start: 0.7641 (t0) cc_final: 0.7337 (t0) REVERT: V 65 GLN cc_start: 0.8395 (mp10) cc_final: 0.8182 (mm-40) REVERT: V 194 ASP cc_start: 0.7995 (m-30) cc_final: 0.7771 (m-30) REVERT: k 107 LYS cc_start: 0.6466 (pttt) cc_final: 0.5768 (ptmt) REVERT: k 114 ILE cc_start: 0.7180 (mp) cc_final: 0.6819 (mp) outliers start: 64 outliers final: 37 residues processed: 548 average time/residue: 0.4435 time to fit residues: 369.6593 Evaluate side-chains 528 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 485 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 371 ASP Chi-restraints excluded: chain x residue 472 PHE Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain x residue 480 GLN Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 75 LYS Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain Z residue 216 GLU Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 66 LEU Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain f residue 60 THR Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 151 ASN Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 139 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 85 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN x 429 ASN X 62 GLN m 48 HIS b 32 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 30250 Z= 0.458 Angle : 0.677 15.665 43276 Z= 0.355 Chirality : 0.045 0.284 5274 Planarity : 0.005 0.128 3668 Dihedral : 21.587 152.578 10453 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.65 % Allowed : 19.91 % Favored : 75.43 % 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: -1.55 (0.16), residues: 2292 helix: 0.46 (0.19), residues: 733 sheet: -1.46 (0.22), residues: 457 loop : -1.87 (0.16), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 177 HIS 0.006 0.001 HIS d 42 PHE 0.018 0.002 PHE a 67 TYR 0.017 0.002 TYR c 194 ARG 0.006 0.001 ARG k 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 492 time to evaluate : 2.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 391 PHE cc_start: 0.4534 (m-80) cc_final: 0.3999 (m-10) REVERT: x 414 LEU cc_start: 0.8677 (tp) cc_final: 0.8375 (tp) REVERT: x 446 GLU cc_start: 0.8199 (tp30) cc_final: 0.7937 (tp30) REVERT: c 113 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8081 (t80) REVERT: c 132 TRP cc_start: 0.9161 (OUTLIER) cc_final: 0.8299 (m100) REVERT: c 139 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8151 (ttpp) REVERT: c 269 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8080 (tm-30) REVERT: n 31 ARG cc_start: 0.8338 (ptm160) cc_final: 0.7872 (ttm110) REVERT: h 19 ARG cc_start: 0.7806 (mtp180) cc_final: 0.7454 (mmt180) REVERT: o 306 ASP cc_start: 0.7667 (m-30) cc_final: 0.7402 (t0) REVERT: i 54 LYS cc_start: 0.9155 (ttmt) cc_final: 0.8849 (ttmt) REVERT: i 56 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.6670 (t0) REVERT: b 64 LYS cc_start: 0.8532 (tttt) cc_final: 0.8182 (ttpp) REVERT: Z 40 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7532 (ttp-170) REVERT: d 29 LYS cc_start: 0.7964 (ttmt) cc_final: 0.7472 (tptt) REVERT: e 94 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8416 (mtmm) REVERT: f 83 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.8309 (t80) REVERT: V 36 GLN cc_start: 0.8561 (tp-100) cc_final: 0.8231 (tp40) REVERT: V 44 LYS cc_start: 0.8911 (ttpp) cc_final: 0.8685 (ttpp) REVERT: V 194 ASP cc_start: 0.8012 (m-30) cc_final: 0.7772 (m-30) REVERT: k 107 LYS cc_start: 0.7039 (pttt) cc_final: 0.6159 (ptmt) REVERT: k 114 ILE cc_start: 0.7151 (mp) cc_final: 0.6618 (mp) outliers start: 86 outliers final: 65 residues processed: 545 average time/residue: 0.4709 time to fit residues: 392.5136 Evaluate side-chains 554 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 484 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 291 THR Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 429 ASN Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain x residue 480 GLN Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain h residue 75 LYS Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 20 VAL Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 60 THR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 151 ASN Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 29 ASN Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 248 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 120 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 chunk 252 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN x 429 ASN c 159 ASN m 46 GLN b 32 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30250 Z= 0.331 Angle : 0.611 15.423 43276 Z= 0.322 Chirality : 0.041 0.273 5274 Planarity : 0.005 0.126 3668 Dihedral : 21.538 155.402 10450 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.36 % Allowed : 20.40 % Favored : 74.24 % 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: -1.32 (0.17), residues: 2292 helix: 0.65 (0.19), residues: 733 sheet: -1.27 (0.23), residues: 444 loop : -1.77 (0.17), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 177 HIS 0.004 0.001 HIS d 42 PHE 0.018 0.001 PHE x 324 TYR 0.017 0.001 TYR x 431 ARG 0.005 0.000 ARG V 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 494 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 391 PHE cc_start: 0.4478 (m-80) cc_final: 0.3991 (m-10) REVERT: x 414 LEU cc_start: 0.8642 (tp) cc_final: 0.8365 (tp) REVERT: x 446 GLU cc_start: 0.8265 (tp30) cc_final: 0.7979 (tp30) REVERT: c 113 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8154 (t80) REVERT: c 132 TRP cc_start: 0.9130 (OUTLIER) cc_final: 0.8334 (m100) REVERT: c 269 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8022 (tm-30) REVERT: n 31 ARG cc_start: 0.8286 (ptm160) cc_final: 0.7798 (ttm110) REVERT: h 19 ARG cc_start: 0.7784 (mtp180) cc_final: 0.7459 (mmt180) REVERT: m 124 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7999 (tt) REVERT: i 54 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8891 (ttpt) REVERT: i 56 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6578 (t0) REVERT: b 64 LYS cc_start: 0.8513 (tttt) cc_final: 0.8139 (ttpp) REVERT: Z 40 ARG cc_start: 0.8027 (ttm170) cc_final: 0.7550 (ttp-170) REVERT: Z 179 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6900 (tt0) REVERT: d 29 LYS cc_start: 0.7975 (ttmt) cc_final: 0.7496 (tptt) REVERT: e 94 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8435 (mtmm) REVERT: f 83 PHE cc_start: 0.9367 (OUTLIER) cc_final: 0.8266 (t80) REVERT: V 36 GLN cc_start: 0.8568 (tp-100) cc_final: 0.8180 (tp40) REVERT: V 37 ASP cc_start: 0.7745 (t0) cc_final: 0.7451 (t0) REVERT: V 44 LYS cc_start: 0.8856 (ttpp) cc_final: 0.8600 (ttpp) REVERT: V 194 ASP cc_start: 0.8018 (m-30) cc_final: 0.7782 (m-30) REVERT: k 107 LYS cc_start: 0.6717 (pttt) cc_final: 0.5885 (ptmt) REVERT: k 114 ILE cc_start: 0.7171 (mp) cc_final: 0.6646 (mp) REVERT: k 132 MET cc_start: 0.7708 (mtp) cc_final: 0.7482 (mtp) outliers start: 99 outliers final: 74 residues processed: 551 average time/residue: 0.4418 time to fit residues: 369.2952 Evaluate side-chains 569 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 489 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 472 PHE Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain x residue 480 GLN Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 116 ASP Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 277 THR Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain n residue 52 GLU Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 14 LEU Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 46 GLN Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 65 LYS Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain d residue 138 VAL Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 58 LEU Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 96 SER Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 151 ASN Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 222 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 199 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 185 optimal weight: 0.2980 chunk 0 optimal weight: 40.0000 chunk 136 optimal weight: 0.5980 chunk 240 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN m 46 GLN b 32 GLN d 137 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30250 Z= 0.249 Angle : 0.578 15.523 43276 Z= 0.305 Chirality : 0.039 0.231 5274 Planarity : 0.004 0.124 3668 Dihedral : 21.500 158.372 10450 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.98 % Allowed : 21.54 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2292 helix: 0.88 (0.20), residues: 727 sheet: -1.13 (0.23), residues: 444 loop : -1.66 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 177 HIS 0.008 0.001 HIS c 191 PHE 0.019 0.001 PHE x 324 TYR 0.016 0.001 TYR x 431 ARG 0.006 0.000 ARG V 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 507 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 391 PHE cc_start: 0.4574 (m-80) cc_final: 0.4113 (m-10) REVERT: x 414 LEU cc_start: 0.8582 (tp) cc_final: 0.8290 (tp) REVERT: x 446 GLU cc_start: 0.8270 (tp30) cc_final: 0.8000 (tp30) REVERT: c 113 PHE cc_start: 0.9305 (OUTLIER) cc_final: 0.8201 (t80) REVERT: c 132 TRP cc_start: 0.9105 (OUTLIER) cc_final: 0.8335 (m100) REVERT: c 139 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8111 (ttpp) REVERT: c 269 GLU cc_start: 0.8323 (tm-30) cc_final: 0.8040 (tm-30) REVERT: n 31 ARG cc_start: 0.8245 (ptm160) cc_final: 0.7800 (ttm110) REVERT: h 19 ARG cc_start: 0.7763 (mtp180) cc_final: 0.7448 (mmt180) REVERT: m 117 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: i 54 LYS cc_start: 0.9094 (ttmt) cc_final: 0.8866 (ttpt) REVERT: i 56 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6531 (t0) REVERT: b 62 LYS cc_start: 0.9038 (tttm) cc_final: 0.8754 (ttmt) REVERT: Z 40 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7567 (ttp-170) REVERT: Z 179 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6911 (tt0) REVERT: d 29 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7500 (tptt) REVERT: e 94 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8374 (mtmm) REVERT: f 83 PHE cc_start: 0.9332 (OUTLIER) cc_final: 0.8168 (t80) REVERT: V 36 GLN cc_start: 0.8555 (tp-100) cc_final: 0.8120 (tp40) REVERT: V 37 ASP cc_start: 0.7606 (t0) cc_final: 0.7324 (t0) REVERT: V 44 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8623 (ttpp) REVERT: V 194 ASP cc_start: 0.7999 (m-30) cc_final: 0.7786 (m-30) REVERT: k 107 LYS cc_start: 0.6610 (pttt) cc_final: 0.5926 (ptmt) REVERT: k 114 ILE cc_start: 0.7028 (mp) cc_final: 0.6681 (mp) REVERT: k 132 MET cc_start: 0.7639 (mtp) cc_final: 0.7302 (mtp) outliers start: 92 outliers final: 68 residues processed: 570 average time/residue: 0.4445 time to fit residues: 386.5106 Evaluate side-chains 572 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 497 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 467 LEU Chi-restraints excluded: chain x residue 480 GLN Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 116 ASP Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 277 THR Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 117 GLU Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain Z residue 16 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 60 THR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 96 SER Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 151 ASN Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 90 optimal weight: 3.9990 chunk 241 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 157 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN b 32 GLN b 41 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 30250 Z= 0.298 Angle : 0.598 15.465 43276 Z= 0.314 Chirality : 0.040 0.224 5274 Planarity : 0.004 0.124 3668 Dihedral : 21.468 157.890 10444 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 5.52 % Allowed : 22.24 % Favored : 72.24 % 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: -1.00 (0.17), residues: 2292 helix: 0.92 (0.20), residues: 725 sheet: -0.98 (0.23), residues: 431 loop : -1.60 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 177 HIS 0.008 0.001 HIS c 191 PHE 0.019 0.001 PHE x 477 TYR 0.023 0.001 TYR x 431 ARG 0.006 0.000 ARG V 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 500 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: x 391 PHE cc_start: 0.4609 (m-80) cc_final: 0.4099 (m-10) REVERT: x 414 LEU cc_start: 0.8585 (tp) cc_final: 0.8294 (tp) REVERT: x 446 GLU cc_start: 0.8265 (tp30) cc_final: 0.7995 (tp30) REVERT: c 113 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8163 (t80) REVERT: c 132 TRP cc_start: 0.9124 (OUTLIER) cc_final: 0.8331 (m100) REVERT: c 139 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8147 (ttpp) REVERT: c 269 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8023 (tm-30) REVERT: n 31 ARG cc_start: 0.8241 (ptm160) cc_final: 0.7794 (ttm110) REVERT: h 19 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7465 (mmt180) REVERT: m 76 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6956 (mm) REVERT: m 117 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6890 (tm-30) REVERT: i 54 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8883 (ttpt) REVERT: i 56 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6596 (t0) REVERT: b 62 LYS cc_start: 0.9029 (tttm) cc_final: 0.8744 (ttmt) REVERT: b 93 MET cc_start: 0.9019 (mmm) cc_final: 0.8816 (mmm) REVERT: Z 179 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6918 (tt0) REVERT: d 29 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7501 (tptt) REVERT: e 94 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8367 (mtmm) REVERT: f 83 PHE cc_start: 0.9326 (OUTLIER) cc_final: 0.8170 (t80) REVERT: V 36 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8110 (tp40) REVERT: V 44 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8578 (ttpp) REVERT: V 194 ASP cc_start: 0.8009 (m-30) cc_final: 0.7795 (m-30) REVERT: k 107 LYS cc_start: 0.6641 (pttt) cc_final: 0.5931 (ptmt) REVERT: k 114 ILE cc_start: 0.7098 (mp) cc_final: 0.6727 (mp) outliers start: 102 outliers final: 79 residues processed: 563 average time/residue: 0.4604 time to fit residues: 394.1078 Evaluate side-chains 587 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 500 time to evaluate : 2.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 291 THR Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 398 ASN Chi-restraints excluded: chain x residue 467 LEU Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 116 ASP Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 277 THR Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain c residue 288 SER Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 58 THR Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 14 LEU Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 15 ASN Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 76 LEU Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 117 GLU Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain b residue 65 LYS Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 96 SER Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 151 ASN Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 258 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 152 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 225 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 266 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN a 73 ASN m 46 GLN b 32 GLN d 137 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 30250 Z= 0.222 Angle : 0.572 15.527 43276 Z= 0.301 Chirality : 0.039 0.212 5274 Planarity : 0.004 0.122 3668 Dihedral : 21.440 159.514 10444 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 5.03 % Allowed : 23.38 % Favored : 71.59 % 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: -0.82 (0.17), residues: 2292 helix: 1.11 (0.20), residues: 720 sheet: -0.92 (0.24), residues: 423 loop : -1.50 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP c 177 HIS 0.006 0.001 HIS c 191 PHE 0.022 0.001 PHE x 324 TYR 0.021 0.001 TYR x 431 ARG 0.007 0.000 ARG V 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 500 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 391 PHE cc_start: 0.4711 (m-80) cc_final: 0.4211 (m-10) REVERT: x 446 GLU cc_start: 0.8188 (tp30) cc_final: 0.7916 (tp30) REVERT: x 472 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.5490 (p90) REVERT: c 113 PHE cc_start: 0.9299 (OUTLIER) cc_final: 0.8236 (t80) REVERT: c 132 TRP cc_start: 0.9085 (OUTLIER) cc_final: 0.8391 (m100) REVERT: c 139 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8085 (ttpp) REVERT: n 31 ARG cc_start: 0.8148 (ptm160) cc_final: 0.7751 (ttm110) REVERT: X 26 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7693 (p0) REVERT: h 19 ARG cc_start: 0.7739 (mtp180) cc_final: 0.7442 (mmt180) REVERT: o 286 SER cc_start: 0.5518 (OUTLIER) cc_final: 0.5278 (t) REVERT: m 76 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6924 (mm) REVERT: m 88 TRP cc_start: 0.8434 (m-10) cc_final: 0.7992 (m-10) REVERT: i 54 LYS cc_start: 0.9076 (ttmt) cc_final: 0.8849 (ttpt) REVERT: i 56 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6507 (t0) REVERT: b 62 LYS cc_start: 0.9009 (tttm) cc_final: 0.8760 (ttmt) REVERT: Z 179 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6923 (tt0) REVERT: d 29 LYS cc_start: 0.7980 (ttmt) cc_final: 0.7497 (tptt) REVERT: e 94 LYS cc_start: 0.8714 (mtpt) cc_final: 0.8387 (mtmm) REVERT: f 83 PHE cc_start: 0.9294 (OUTLIER) cc_final: 0.8021 (t80) REVERT: V 36 GLN cc_start: 0.8500 (tp-100) cc_final: 0.7973 (tp40) REVERT: V 44 LYS cc_start: 0.8900 (ttpp) cc_final: 0.8667 (ttpp) REVERT: V 194 ASP cc_start: 0.7995 (m-30) cc_final: 0.7784 (m-30) REVERT: k 107 LYS cc_start: 0.6617 (pttt) cc_final: 0.5917 (ptmt) REVERT: k 114 ILE cc_start: 0.7224 (mp) cc_final: 0.6907 (mp) outliers start: 93 outliers final: 72 residues processed: 556 average time/residue: 0.4625 time to fit residues: 392.2391 Evaluate side-chains 581 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 499 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 467 LEU Chi-restraints excluded: chain x residue 472 PHE Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 116 ASP Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 277 THR Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 26 ASN Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 17 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 60 GLU Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 76 LEU Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain Z residue 16 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 96 SER Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 151 ASN Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 165 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 159 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 209 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN m 46 GLN b 32 GLN b 41 GLN d 137 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30250 Z= 0.216 Angle : 0.568 15.453 43276 Z= 0.298 Chirality : 0.038 0.211 5274 Planarity : 0.004 0.122 3668 Dihedral : 21.398 160.513 10444 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 5.41 % Allowed : 23.05 % Favored : 71.54 % 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: -0.74 (0.17), residues: 2292 helix: 1.20 (0.20), residues: 721 sheet: -0.89 (0.23), residues: 443 loop : -1.45 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 291 HIS 0.005 0.001 HIS c 191 PHE 0.030 0.001 PHE x 324 TYR 0.022 0.001 TYR x 431 ARG 0.008 0.000 ARG V 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 513 time to evaluate : 2.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 302 ASP cc_start: 0.5388 (m-30) cc_final: 0.5020 (t0) REVERT: x 391 PHE cc_start: 0.4698 (m-80) cc_final: 0.4229 (m-10) REVERT: x 446 GLU cc_start: 0.8179 (tp30) cc_final: 0.7909 (tp30) REVERT: c 113 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8233 (t80) REVERT: c 132 TRP cc_start: 0.9098 (OUTLIER) cc_final: 0.8394 (m100) REVERT: c 139 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8069 (ttpp) REVERT: n 31 ARG cc_start: 0.8129 (ptm160) cc_final: 0.7729 (ttm110) REVERT: n 60 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7692 (tm-30) REVERT: X 26 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7666 (p0) REVERT: h 19 ARG cc_start: 0.7782 (mtp180) cc_final: 0.7501 (mmt180) REVERT: o 286 SER cc_start: 0.5516 (OUTLIER) cc_final: 0.5286 (t) REVERT: a 25 LYS cc_start: 0.8735 (tttt) cc_final: 0.8464 (tttp) REVERT: m 29 ASP cc_start: 0.7911 (t0) cc_final: 0.7680 (t0) REVERT: m 76 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6884 (mm) REVERT: m 88 TRP cc_start: 0.8425 (m-10) cc_final: 0.7967 (m-10) REVERT: m 132 LYS cc_start: 0.3890 (OUTLIER) cc_final: 0.3407 (ttpt) REVERT: i 54 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8841 (ttpt) REVERT: i 56 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6506 (t0) REVERT: b 34 MET cc_start: 0.8726 (mtt) cc_final: 0.8486 (mtp) REVERT: b 62 LYS cc_start: 0.9002 (tttm) cc_final: 0.8760 (ttmt) REVERT: Z 47 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7444 (mt-10) REVERT: Z 179 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: d 29 LYS cc_start: 0.7992 (ttmt) cc_final: 0.7478 (tptt) REVERT: e 94 LYS cc_start: 0.8690 (mtpt) cc_final: 0.8348 (mtmm) REVERT: f 83 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.7943 (t80) REVERT: V 36 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8033 (tp40) REVERT: V 44 LYS cc_start: 0.8831 (ttpp) cc_final: 0.8584 (ttpp) REVERT: V 194 ASP cc_start: 0.7993 (m-30) cc_final: 0.7782 (m-30) REVERT: k 107 LYS cc_start: 0.6619 (pttt) cc_final: 0.5910 (ptmt) REVERT: k 114 ILE cc_start: 0.7230 (mp) cc_final: 0.6924 (mp) outliers start: 100 outliers final: 72 residues processed: 574 average time/residue: 0.4428 time to fit residues: 388.5601 Evaluate side-chains 591 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 509 time to evaluate : 2.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 467 LEU Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 115 SER Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 153 CYS Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain c residue 288 SER Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 26 ASN Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 39 LEU Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 76 LEU Chi-restraints excluded: chain m residue 80 ASP Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain m residue 132 LYS Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain Z residue 16 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 96 SER Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 151 ASN Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 242 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 195 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 224 optimal weight: 0.4980 chunk 235 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN h 100 GLN b 32 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 30250 Z= 0.383 Angle : 0.642 15.649 43276 Z= 0.335 Chirality : 0.042 0.227 5274 Planarity : 0.005 0.125 3668 Dihedral : 21.447 155.576 10443 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.03 % Allowed : 23.76 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2292 helix: 1.02 (0.20), residues: 725 sheet: -0.79 (0.24), residues: 437 loop : -1.55 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 291 HIS 0.006 0.001 HIS c 191 PHE 0.031 0.002 PHE x 324 TYR 0.024 0.002 TYR x 431 ARG 0.009 0.000 ARG V 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 499 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 302 ASP cc_start: 0.5359 (m-30) cc_final: 0.5039 (t0) REVERT: x 391 PHE cc_start: 0.4680 (m-80) cc_final: 0.4219 (m-10) REVERT: x 446 GLU cc_start: 0.8276 (tp30) cc_final: 0.7964 (tp30) REVERT: c 132 TRP cc_start: 0.9150 (OUTLIER) cc_final: 0.8246 (m100) REVERT: c 139 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8205 (ttpp) REVERT: n 31 ARG cc_start: 0.8199 (ptm160) cc_final: 0.7759 (ttm110) REVERT: X 26 ASN cc_start: 0.8257 (OUTLIER) cc_final: 0.7799 (p0) REVERT: h 19 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7429 (ttm170) REVERT: m 29 ASP cc_start: 0.7983 (t0) cc_final: 0.7737 (t0) REVERT: m 76 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6894 (mm) REVERT: m 88 TRP cc_start: 0.8549 (m-10) cc_final: 0.8015 (m-10) REVERT: m 132 LYS cc_start: 0.3862 (OUTLIER) cc_final: 0.3373 (ttpt) REVERT: i 54 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8878 (ttpt) REVERT: i 56 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6606 (t0) REVERT: b 62 LYS cc_start: 0.9036 (tttm) cc_final: 0.8768 (ttmt) REVERT: Z 47 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7417 (mt-10) REVERT: Z 179 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: d 29 LYS cc_start: 0.8003 (ttmt) cc_final: 0.7511 (tptt) REVERT: e 94 LYS cc_start: 0.8754 (mtpt) cc_final: 0.8446 (mtmm) REVERT: f 83 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8095 (t80) REVERT: V 36 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8106 (tp40) REVERT: V 44 LYS cc_start: 0.8985 (ttpp) cc_final: 0.8674 (ttpp) REVERT: V 194 ASP cc_start: 0.7981 (m-30) cc_final: 0.7774 (m-30) outliers start: 93 outliers final: 78 residues processed: 556 average time/residue: 0.4490 time to fit residues: 379.8198 Evaluate side-chains 582 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 496 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 291 THR Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 467 LEU Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 209 SER Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain c residue 288 SER Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 26 ASN Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 76 LEU Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain m residue 132 LYS Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain Z residue 16 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 74 SER Chi-restraints excluded: chain e residue 99 LEU Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 68 ILE Chi-restraints excluded: chain f residue 71 MET Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 96 SER Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain V residue 196 LEU Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 151 ASN Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 163 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 124 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 327 GLN h 100 GLN a 73 ASN b 32 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30250 Z= 0.260 Angle : 0.593 15.355 43276 Z= 0.311 Chirality : 0.039 0.215 5274 Planarity : 0.004 0.123 3668 Dihedral : 21.424 158.727 10443 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.82 % Allowed : 24.03 % Favored : 71.16 % 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: -0.75 (0.17), residues: 2292 helix: 1.11 (0.20), residues: 727 sheet: -0.70 (0.25), residues: 408 loop : -1.50 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 291 HIS 0.006 0.001 HIS c 191 PHE 0.030 0.001 PHE x 324 TYR 0.022 0.001 TYR x 431 ARG 0.009 0.000 ARG V 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4584 Ramachandran restraints generated. 2292 Oldfield, 0 Emsley, 2292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 516 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: x 302 ASP cc_start: 0.5328 (m-30) cc_final: 0.4982 (t0) REVERT: x 327 GLN cc_start: 0.6591 (tt0) cc_final: 0.6279 (tt0) REVERT: x 330 ARG cc_start: 0.5736 (mmm160) cc_final: 0.5471 (mmm160) REVERT: x 360 ARG cc_start: 0.6714 (mtp180) cc_final: 0.6466 (mtm110) REVERT: x 391 PHE cc_start: 0.4661 (m-80) cc_final: 0.4196 (m-10) REVERT: x 480 GLN cc_start: 0.6873 (tt0) cc_final: 0.6580 (mt0) REVERT: c 113 PHE cc_start: 0.9289 (OUTLIER) cc_final: 0.8184 (t80) REVERT: c 118 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8052 (mmm-85) REVERT: c 132 TRP cc_start: 0.9103 (OUTLIER) cc_final: 0.8321 (m100) REVERT: c 139 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8111 (ttpp) REVERT: c 218 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8608 (mp) REVERT: n 31 ARG cc_start: 0.8157 (ptm160) cc_final: 0.7747 (ttm110) REVERT: X 26 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7775 (p0) REVERT: h 19 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7466 (mmt180) REVERT: o 286 SER cc_start: 0.5519 (OUTLIER) cc_final: 0.5286 (t) REVERT: m 29 ASP cc_start: 0.7947 (t0) cc_final: 0.7700 (t0) REVERT: m 76 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6894 (mm) REVERT: m 88 TRP cc_start: 0.8435 (m-10) cc_final: 0.8005 (m-10) REVERT: m 132 LYS cc_start: 0.3797 (OUTLIER) cc_final: 0.3303 (ttpt) REVERT: i 54 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8861 (ttpt) REVERT: i 56 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6539 (t0) REVERT: b 34 MET cc_start: 0.8755 (mtt) cc_final: 0.8517 (mtp) REVERT: b 62 LYS cc_start: 0.8985 (tttm) cc_final: 0.8742 (ttmt) REVERT: Z 47 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7421 (mt-10) REVERT: Z 179 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: d 29 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7499 (tptt) REVERT: e 94 LYS cc_start: 0.8748 (mtpt) cc_final: 0.8418 (mtmm) REVERT: f 83 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.7993 (t80) REVERT: V 36 GLN cc_start: 0.8556 (tp-100) cc_final: 0.7978 (tp-100) REVERT: V 44 LYS cc_start: 0.8971 (ttpp) cc_final: 0.8649 (ttpp) REVERT: V 194 ASP cc_start: 0.8004 (m-30) cc_final: 0.7798 (m-30) REVERT: k 107 LYS cc_start: 0.6541 (pttt) cc_final: 0.5879 (ptmt) outliers start: 89 outliers final: 74 residues processed: 568 average time/residue: 0.4465 time to fit residues: 386.5005 Evaluate side-chains 600 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 515 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain x residue 291 THR Chi-restraints excluded: chain x residue 318 THR Chi-restraints excluded: chain x residue 382 MET Chi-restraints excluded: chain x residue 386 ASN Chi-restraints excluded: chain x residue 467 LEU Chi-restraints excluded: chain x residue 476 GLU Chi-restraints excluded: chain c residue 6 THR Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 33 SER Chi-restraints excluded: chain c residue 35 SER Chi-restraints excluded: chain c residue 97 THR Chi-restraints excluded: chain c residue 107 ASP Chi-restraints excluded: chain c residue 113 PHE Chi-restraints excluded: chain c residue 132 TRP Chi-restraints excluded: chain c residue 139 LYS Chi-restraints excluded: chain c residue 142 VAL Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 192 THR Chi-restraints excluded: chain c residue 217 MET Chi-restraints excluded: chain c residue 218 LEU Chi-restraints excluded: chain c residue 246 TYR Chi-restraints excluded: chain c residue 274 VAL Chi-restraints excluded: chain c residue 287 THR Chi-restraints excluded: chain c residue 288 SER Chi-restraints excluded: chain n residue 17 VAL Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 28 THR Chi-restraints excluded: chain X residue 8 THR Chi-restraints excluded: chain X residue 26 ASN Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 71 ILE Chi-restraints excluded: chain X residue 73 LEU Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain o residue 240 THR Chi-restraints excluded: chain o residue 286 SER Chi-restraints excluded: chain o residue 297 ILE Chi-restraints excluded: chain a residue 27 VAL Chi-restraints excluded: chain a residue 90 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 76 LEU Chi-restraints excluded: chain m residue 91 LEU Chi-restraints excluded: chain m residue 123 VAL Chi-restraints excluded: chain m residue 124 ILE Chi-restraints excluded: chain m residue 132 LYS Chi-restraints excluded: chain i residue 9 SER Chi-restraints excluded: chain i residue 30 LEU Chi-restraints excluded: chain i residue 56 ASP Chi-restraints excluded: chain b residue 20 VAL Chi-restraints excluded: chain Z residue 16 ILE Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 104 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 139 SER Chi-restraints excluded: chain Z residue 143 ARG Chi-restraints excluded: chain Z residue 149 SER Chi-restraints excluded: chain Z residue 156 LEU Chi-restraints excluded: chain Z residue 179 GLN Chi-restraints excluded: chain Z residue 197 LYS Chi-restraints excluded: chain Z residue 209 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 8 ASP Chi-restraints excluded: chain d residue 15 VAL Chi-restraints excluded: chain d residue 34 VAL Chi-restraints excluded: chain d residue 63 HIS Chi-restraints excluded: chain d residue 96 SER Chi-restraints excluded: chain e residue 51 ASP Chi-restraints excluded: chain e residue 110 THR Chi-restraints excluded: chain f residue 53 THR Chi-restraints excluded: chain f residue 68 ILE Chi-restraints excluded: chain f residue 73 ASN Chi-restraints excluded: chain f residue 83 PHE Chi-restraints excluded: chain f residue 96 SER Chi-restraints excluded: chain f residue 117 ILE Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 136 THR Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 73 THR Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 187 SER Chi-restraints excluded: chain k residue 103 LEU Chi-restraints excluded: chain k residue 117 LEU Chi-restraints excluded: chain k residue 151 ASN Chi-restraints excluded: chain Y residue 20 THR Chi-restraints excluded: chain Y residue 31 LEU Chi-restraints excluded: chain Y residue 97 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 277 random chunks: chunk 174 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 67 optimal weight: 0.0470 chunk 202 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 92 optimal weight: 0.0970 chunk 226 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: h 100 GLN m 19 GLN b 41 GLN ** V 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 11 GLN Y 86 GLN ** Y 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.081665 restraints weight = 47322.056| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.65 r_work: 0.2758 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30250 Z= 0.190 Angle : 0.572 15.633 43276 Z= 0.300 Chirality : 0.038 0.213 5274 Planarity : 0.004 0.121 3668 Dihedral : 21.403 161.310 10443 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 4.44 % Allowed : 24.68 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.17), residues: 2292 helix: 1.30 (0.20), residues: 719 sheet: -0.68 (0.25), residues: 413 loop : -1.43 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP c 177 HIS 0.005 0.001 HIS c 191 PHE 0.030 0.001 PHE x 324 TYR 0.021 0.001 TYR x 431 ARG 0.006 0.000 ARG Z 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7829.48 seconds wall clock time: 141 minutes 56.93 seconds (8516.93 seconds total)