Starting phenix.real_space_refine on Sat Mar 16 14:56:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmt_22928/03_2024/7kmt_22928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmt_22928/03_2024/7kmt_22928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmt_22928/03_2024/7kmt_22928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmt_22928/03_2024/7kmt_22928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmt_22928/03_2024/7kmt_22928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kmt_22928/03_2024/7kmt_22928_updated.pdb" } resolution = 3.7 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= 0.003 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: 4 Type Number sf(0) Gaussians S 89 5.16 5 C 9635 2.51 5 N 2450 2.21 5 O 2771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 4": "OE1" <-> "OE2" Residue "H ASP 24": "OD1" <-> "OD2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 105": "OD1" <-> "OD2" Residue "H PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 125": "OD1" <-> "OD2" Residue "H TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 176": "OD1" <-> "OD2" Residue "H ARG 180": "NH1" <-> "NH2" Residue "H TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 209": "OE1" <-> "OE2" Residue "H GLU 216": "OE1" <-> "OE2" Residue "J GLU 48": "OE1" <-> "OE2" Residue "J ASP 82": "OD1" <-> "OD2" Residue "J PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 105": "NH1" <-> "NH2" Residue "J ARG 172": "NH1" <-> "NH2" Residue "J ASP 173": "OD1" <-> "OD2" Residue "J PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 127": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "I GLU 23": "OE1" <-> "OE2" Residue "I ARG 47": "NH1" <-> "NH2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 88": "OE1" <-> "OE2" Residue "I ASP 160": "OD1" <-> "OD2" Residue "I ARG 169": "NH1" <-> "NH2" Residue "I GLU 175": "OE1" <-> "OE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F ASP 48": "OD1" <-> "OD2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F GLU 129": "OE1" <-> "OE2" Residue "F TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 169": "NH1" <-> "NH2" Residue "F GLU 175": "OE1" <-> "OE2" Residue "E TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E GLU 91": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 223": "NH1" <-> "NH2" Residue "E TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 12": "OD1" <-> "OD2" Residue "K GLU 17": "OE1" <-> "OE2" Residue "K ASP 32": "OD1" <-> "OD2" Residue "K ASP 85": "OD1" <-> "OD2" Residue "K TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 157": "NH1" <-> "NH2" Residue "K ASP 162": "OD1" <-> "OD2" Residue "A ASP 6": "OD1" <-> "OD2" Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A GLU 51": "OE1" <-> "OE2" Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "B TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B PHE 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 614": "OE1" <-> "OE2" Residue "B ARG 620": "NH1" <-> "NH2" Residue "B PHE 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14945 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1352 Classifications: {'peptide': 169} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 162} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1553 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain breaks: 1 Chain: "G" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1273 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "I" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1467 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "F" Number of atoms: 1467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1467 Classifications: {'peptide': 182} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain: "E" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1454 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain breaks: 4 Chain: "K" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1081 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain breaks: 3 Chain: "A" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1385 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 1, 'TRANS': 172} Chain breaks: 5 Chain: "B" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3879 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 17, 'TRANS': 457} Chain breaks: 16 Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 7.91, per 1000 atoms: 0.53 Number of scatterers: 14945 At special positions: 0 Unit cell: (95.082, 111.618, 230.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 89 16.00 O 2771 8.00 N 2450 7.00 C 9635 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.90 Conformation dependent library (CDL) restraints added in 3.1 seconds 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3524 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 9 sheets defined 46.4% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'H' and resid 30 through 48 Processing helix chain 'H' and resid 170 through 189 Processing helix chain 'H' and resid 205 through 218 Processing helix chain 'J' and resid 59 through 76 removed outlier: 3.721A pdb=" N THR J 76 " --> pdb=" O GLN J 72 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 107 removed outlier: 4.267A pdb=" N GLU J 100 " --> pdb=" O ILE J 96 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER J 107 " --> pdb=" O ASN J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'J' and resid 176 through 185 Processing helix chain 'J' and resid 187 through 191 Processing helix chain 'J' and resid 227 through 244 removed outlier: 3.696A pdb=" N TYR J 231 " --> pdb=" O SER J 228 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE J 232 " --> pdb=" O CYS J 229 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY J 239 " --> pdb=" O ILE J 236 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN J 243 " --> pdb=" O PHE J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 272 through 280 Processing helix chain 'G' and resid 35 through 57 removed outlier: 4.189A pdb=" N GLU G 39 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 109 Processing helix chain 'G' and resid 111 through 114 No H-bonds generated for 'chain 'G' and resid 111 through 114' Processing helix chain 'G' and resid 129 through 132 No H-bonds generated for 'chain 'G' and resid 129 through 132' Processing helix chain 'G' and resid 143 through 156 Proline residue: G 155 - end of helix Processing helix chain 'I' and resid 10 through 20 Processing helix chain 'I' and resid 27 through 44 Processing helix chain 'I' and resid 49 through 75 removed outlier: 3.830A pdb=" N ARG I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU I 69 " --> pdb=" O CYS I 65 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP I 70 " --> pdb=" O ARG I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 97 removed outlier: 5.213A pdb=" N PHE I 95 " --> pdb=" O SER I 91 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LYS I 96 " --> pdb=" O LYS I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 112 No H-bonds generated for 'chain 'I' and resid 110 through 112' Processing helix chain 'I' and resid 123 through 125 No H-bonds generated for 'chain 'I' and resid 123 through 125' Processing helix chain 'I' and resid 140 through 153 removed outlier: 4.631A pdb=" N ILE I 143 " --> pdb=" O TYR I 140 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL I 147 " --> pdb=" O LEU I 144 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER I 151 " --> pdb=" O LEU I 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 20 Processing helix chain 'F' and resid 27 through 44 removed outlier: 3.908A pdb=" N ASP F 44 " --> pdb=" O GLN F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 74 removed outlier: 3.678A pdb=" N ARG F 66 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU F 69 " --> pdb=" O CYS F 65 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASP F 70 " --> pdb=" O ARG F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'F' and resid 94 through 98 Processing helix chain 'F' and resid 110 through 112 No H-bonds generated for 'chain 'F' and resid 110 through 112' Processing helix chain 'F' and resid 132 through 137 removed outlier: 3.756A pdb=" N LYS F 136 " --> pdb=" O MET F 132 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N SER F 137 " --> pdb=" O ASP F 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 132 through 137' Processing helix chain 'F' and resid 142 through 154 Processing helix chain 'E' and resid 43 through 62 removed outlier: 4.668A pdb=" N VAL E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 113 through 131 Processing helix chain 'E' and resid 158 through 162 removed outlier: 3.747A pdb=" N ARG E 162 " --> pdb=" O PHE E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 168 Processing helix chain 'E' and resid 204 through 226 Proline residue: E 213 - end of helix removed outlier: 4.440A pdb=" N GLU E 216 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) Proline residue: E 218 - end of helix Processing helix chain 'K' and resid 33 through 52 Proline residue: K 38 - end of helix removed outlier: 4.427A pdb=" N ASP K 46 " --> pdb=" O HIS K 42 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE K 47 " --> pdb=" O ALA K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 146 Processing helix chain 'K' and resid 159 through 172 Processing helix chain 'A' and resid 21 through 28 removed outlier: 4.165A pdb=" N ARG A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 removed outlier: 4.874A pdb=" N SER A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 109 removed outlier: 3.828A pdb=" N LYS A 100 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N MET A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ARG A 108 " --> pdb=" O GLN A 104 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 removed outlier: 3.663A pdb=" N ASN A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'B' and resid 6 through 9 No H-bonds generated for 'chain 'B' and resid 6 through 9' Processing helix chain 'B' and resid 26 through 34 Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 60 through 67 removed outlier: 4.231A pdb=" N PHE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 172 Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'B' and resid 225 through 235 Processing helix chain 'B' and resid 268 through 283 Processing helix chain 'B' and resid 316 through 324 removed outlier: 4.280A pdb=" N LEU B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE B 321 " --> pdb=" O GLU B 317 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 324 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 349 Processing helix chain 'B' and resid 352 through 365 Processing helix chain 'B' and resid 415 through 426 Processing helix chain 'B' and resid 430 through 439 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 479 through 496 Processing helix chain 'B' and resid 518 through 529 removed outlier: 3.947A pdb=" N GLU B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 549 Proline residue: B 539 - end of helix Processing helix chain 'B' and resid 556 through 572 removed outlier: 3.905A pdb=" N MET B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 635 Processing helix chain 'B' and resid 639 through 654 removed outlier: 4.493A pdb=" N SER B 651 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR B 652 " --> pdb=" O ASP B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 672 Processing sheet with id= A, first strand: chain 'H' and resid 121 through 124 removed outlier: 3.691A pdb=" N THR H 5 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR H 17 " --> pdb=" O VAL H 8 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'J' and resid 198 through 201 removed outlier: 4.373A pdb=" N ASP J 198 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL J 212 " --> pdb=" O ASP J 198 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 69 through 71 removed outlier: 6.381A pdb=" N ASP G 10 " --> pdb=" O CYS G 15 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS G 15 " --> pdb=" O ASP G 10 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'I' and resid 114 through 118 removed outlier: 7.469A pdb=" N ASP I 158 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 104 through 106 removed outlier: 7.449A pdb=" N ASP F 158 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 175 through 177 Processing sheet with id= G, first strand: chain 'K' and resid 90 through 93 removed outlier: 6.819A pdb=" N ILE K 100 " --> pdb=" O VAL K 92 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.609A pdb=" N TYR A 7 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 64 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY A 15 " --> pdb=" O THR A 64 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 133 through 136 removed outlier: 7.305A pdb=" N THR B 136 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ILE B 39 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR B 40 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER B 213 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 255 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE B 215 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL B 257 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU B 217 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU B 259 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU B 287 " --> pdb=" O PHE B 258 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU B 260 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE B 289 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR B 262 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 291 " --> pdb=" O TYR B 262 " (cutoff:3.500A) 657 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 6.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2448 1.32 - 1.44: 4043 1.44 - 1.57: 8589 1.57 - 1.69: 1 1.69 - 1.82: 142 Bond restraints: 15223 Sorted by residual: bond pdb=" C THR B 538 " pdb=" O THR B 538 " ideal model delta sigma weight residual 1.243 1.192 0.051 9.90e-03 1.02e+04 2.64e+01 bond pdb=" CA SER B 537 " pdb=" CB SER B 537 " ideal model delta sigma weight residual 1.535 1.472 0.063 1.51e-02 4.39e+03 1.74e+01 bond pdb=" CA SER B 411 " pdb=" CB SER B 411 " ideal model delta sigma weight residual 1.536 1.477 0.060 1.46e-02 4.69e+03 1.68e+01 bond pdb=" N SER B 411 " pdb=" CA SER B 411 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.50e-02 4.44e+03 8.91e+00 bond pdb=" N THR B 538 " pdb=" CA THR B 538 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.04e-02 9.25e+03 6.73e+00 ... (remaining 15218 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.24: 207 105.24 - 112.47: 7542 112.47 - 119.70: 5470 119.70 - 126.93: 7134 126.93 - 134.16: 156 Bond angle restraints: 20509 Sorted by residual: angle pdb=" N GLU I 129 " pdb=" CA GLU I 129 " pdb=" C GLU I 129 " ideal model delta sigma weight residual 109.50 98.01 11.49 1.58e+00 4.01e-01 5.29e+01 angle pdb=" CA GLU I 129 " pdb=" C GLU I 129 " pdb=" O GLU I 129 " ideal model delta sigma weight residual 121.11 115.61 5.50 1.17e+00 7.31e-01 2.21e+01 angle pdb=" CA SER B 412 " pdb=" C SER B 412 " pdb=" O SER B 412 " ideal model delta sigma weight residual 121.31 116.37 4.94 1.07e+00 8.73e-01 2.13e+01 angle pdb=" N THR B 538 " pdb=" CA THR B 538 " pdb=" C THR B 538 " ideal model delta sigma weight residual 113.45 107.61 5.84 1.39e+00 5.18e-01 1.77e+01 angle pdb=" N GLU B 414 " pdb=" CA GLU B 414 " pdb=" C GLU B 414 " ideal model delta sigma weight residual 113.61 107.93 5.68 1.50e+00 4.44e-01 1.44e+01 ... (remaining 20504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8093 17.82 - 35.64: 889 35.64 - 53.46: 147 53.46 - 71.28: 22 71.28 - 89.10: 13 Dihedral angle restraints: 9164 sinusoidal: 3762 harmonic: 5402 Sorted by residual: dihedral pdb=" CA SER H 197 " pdb=" C SER H 197 " pdb=" N MET H 198 " pdb=" CA MET H 198 " ideal model delta harmonic sigma weight residual -180.00 -152.39 -27.61 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA ARG B 74 " pdb=" C ARG B 74 " pdb=" N ASP B 75 " pdb=" CA ASP B 75 " ideal model delta harmonic sigma weight residual -180.00 -159.04 -20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA GLN B 636 " pdb=" C GLN B 636 " pdb=" N LYS B 637 " pdb=" CA LYS B 637 " ideal model delta harmonic sigma weight residual -180.00 -159.62 -20.38 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 9161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1816 0.050 - 0.099: 409 0.099 - 0.149: 89 0.149 - 0.199: 6 0.199 - 0.248: 1 Chirality restraints: 2321 Sorted by residual: chirality pdb=" CA GLU I 129 " pdb=" N GLU I 129 " pdb=" C GLU I 129 " pdb=" CB GLU I 129 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CG LEU B 487 " pdb=" CB LEU B 487 " pdb=" CD1 LEU B 487 " pdb=" CD2 LEU B 487 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" CA VAL I 178 " pdb=" N VAL I 178 " pdb=" C VAL I 178 " pdb=" CB VAL I 178 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 2318 not shown) Planarity restraints: 2556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 217 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.11e+00 pdb=" N PRO E 218 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 218 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 218 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET G 47 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C MET G 47 " 0.042 2.00e-02 2.50e+03 pdb=" O MET G 47 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE G 48 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 49 " 0.011 2.00e-02 2.50e+03 2.18e-02 4.75e+00 pdb=" C PHE G 49 " -0.038 2.00e-02 2.50e+03 pdb=" O PHE G 49 " 0.014 2.00e-02 2.50e+03 pdb=" N SER G 50 " 0.013 2.00e-02 2.50e+03 ... (remaining 2553 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 179 2.59 - 3.17: 13586 3.17 - 3.75: 23351 3.75 - 4.32: 31890 4.32 - 4.90: 52489 Nonbonded interactions: 121495 Sorted by model distance: nonbonded pdb=" O VAL F 84 " pdb=" OG SER F 87 " model vdw 2.018 2.440 nonbonded pdb=" OG1 THR G 141 " pdb=" OE1 GLU E 200 " model vdw 2.088 2.440 nonbonded pdb=" OE2 GLU B 25 " pdb=" OG SER B 530 " model vdw 2.101 2.440 nonbonded pdb=" OG SER I 165 " pdb=" O GLN I 173 " model vdw 2.105 2.440 nonbonded pdb=" O LEU F 83 " pdb=" OG1 THR F 86 " model vdw 2.123 2.440 ... (remaining 121490 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'I' } 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 group one per residue 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: 14.180 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: 0.010 Extract box with map and model: 14.590 Check model and map are aligned: 0.290 Set scattering table: 0.150 Process input model: 41.720 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 15223 Z= 0.294 Angle : 0.790 11.492 20509 Z= 0.426 Chirality : 0.044 0.248 2321 Planarity : 0.005 0.062 2556 Dihedral : 15.020 89.099 5640 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1756 helix: 0.37 (0.17), residues: 854 sheet: -1.61 (0.30), residues: 259 loop : -1.45 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 535 HIS 0.007 0.001 HIS E 106 PHE 0.030 0.002 PHE E 242 TYR 0.028 0.002 TYR F 57 ARG 0.015 0.001 ARG K 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.778 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: H 136 THR cc_start: 0.9246 (p) cc_final: 0.9015 (t) REVERT: J 48 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7887 (mt-10) REVERT: J 250 VAL cc_start: 0.9032 (t) cc_final: 0.8764 (p) REVERT: G 64 LYS cc_start: 0.8589 (tttt) cc_final: 0.8373 (tttp) REVERT: F 156 GLN cc_start: 0.9142 (mm110) cc_final: 0.8575 (mt0) REVERT: E 47 MET cc_start: 0.8869 (ppp) cc_final: 0.8596 (ppp) REVERT: E 57 MET cc_start: 0.8656 (tpt) cc_final: 0.8112 (tpt) REVERT: K 49 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8417 (mt-10) REVERT: K 50 ASP cc_start: 0.7975 (t0) cc_final: 0.7770 (t0) REVERT: K 113 MET cc_start: 0.8715 (ppp) cc_final: 0.8467 (ppp) REVERT: K 136 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8341 (mm-30) REVERT: K 154 ASP cc_start: 0.7800 (t0) cc_final: 0.7459 (t0) REVERT: K 171 LYS cc_start: 0.9232 (mttm) cc_final: 0.8953 (mttm) REVERT: A 138 GLU cc_start: 0.8162 (pp20) cc_final: 0.7955 (pp20) REVERT: A 192 ASN cc_start: 0.8330 (t0) cc_final: 0.8006 (t0) REVERT: B 343 LEU cc_start: 0.9220 (mt) cc_final: 0.8922 (mt) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.2942 time to fit residues: 86.2425 Evaluate side-chains 123 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 105 optimal weight: 0.5980 chunk 163 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 243 ASN G 56 GLN G 130 ASN I 181 ASN ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN B 477 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15223 Z= 0.211 Angle : 0.615 10.833 20509 Z= 0.315 Chirality : 0.042 0.172 2321 Planarity : 0.004 0.047 2556 Dihedral : 6.057 57.819 1981 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 0.42 % Allowed : 8.40 % Favored : 91.19 % 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: -0.57 (0.20), residues: 1756 helix: 0.69 (0.18), residues: 854 sheet: -1.29 (0.31), residues: 262 loop : -1.35 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 162 HIS 0.003 0.001 HIS J 253 PHE 0.023 0.001 PHE B 270 TYR 0.020 0.001 TYR F 57 ARG 0.006 0.001 ARG K 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 136 THR cc_start: 0.9273 (p) cc_final: 0.9014 (t) REVERT: H 200 MET cc_start: 0.8995 (mpp) cc_final: 0.8381 (mmm) REVERT: H 214 MET cc_start: 0.9076 (tpp) cc_final: 0.8836 (tpp) REVERT: J 48 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7880 (mt-10) REVERT: J 181 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7832 (tm-30) REVERT: G 64 LYS cc_start: 0.8508 (tttt) cc_final: 0.8289 (tttp) REVERT: G 156 MET cc_start: 0.8637 (mtm) cc_final: 0.8427 (mpp) REVERT: F 156 GLN cc_start: 0.9311 (mm110) cc_final: 0.8849 (mt0) REVERT: E 47 MET cc_start: 0.8944 (ppp) cc_final: 0.8599 (ppp) REVERT: E 52 MET cc_start: 0.9180 (mtm) cc_final: 0.8760 (mtp) REVERT: E 57 MET cc_start: 0.8582 (tpt) cc_final: 0.7781 (tpp) REVERT: K 49 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8296 (mt-10) REVERT: K 127 ASP cc_start: 0.8177 (p0) cc_final: 0.7752 (p0) REVERT: K 136 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8369 (mm-30) REVERT: K 140 LEU cc_start: 0.9384 (mp) cc_final: 0.9166 (mm) REVERT: K 154 ASP cc_start: 0.7631 (t0) cc_final: 0.7264 (t0) REVERT: A 138 GLU cc_start: 0.8201 (pp20) cc_final: 0.7970 (pp20) REVERT: A 192 ASN cc_start: 0.8283 (t0) cc_final: 0.7987 (t0) REVERT: B 343 LEU cc_start: 0.9217 (mt) cc_final: 0.9007 (mt) REVERT: B 464 MET cc_start: 0.8852 (mmm) cc_final: 0.8579 (tpp) outliers start: 7 outliers final: 3 residues processed: 144 average time/residue: 0.2514 time to fit residues: 56.5741 Evaluate side-chains 119 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain B residue 22 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 HIS ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 ASN K 42 HIS K 52 GLN K 128 ASN B 76 GLN B 156 HIS B 209 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 15223 Z= 0.385 Angle : 0.656 11.363 20509 Z= 0.343 Chirality : 0.043 0.172 2321 Planarity : 0.004 0.040 2556 Dihedral : 5.885 56.463 1981 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 1.25 % Allowed : 12.15 % Favored : 86.60 % 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: -0.68 (0.20), residues: 1756 helix: 0.60 (0.18), residues: 861 sheet: -1.18 (0.31), residues: 263 loop : -1.52 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 162 HIS 0.006 0.001 HIS B 188 PHE 0.029 0.002 PHE I 127 TYR 0.020 0.002 TYR F 57 ARG 0.005 0.001 ARG H 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 200 MET cc_start: 0.9053 (mpp) cc_final: 0.8573 (mmm) REVERT: J 48 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7953 (mt-10) REVERT: F 156 GLN cc_start: 0.9346 (mm110) cc_final: 0.8942 (mt0) REVERT: E 47 MET cc_start: 0.8898 (ppp) cc_final: 0.8473 (ppp) REVERT: E 52 MET cc_start: 0.9209 (mtm) cc_final: 0.8745 (mtp) REVERT: E 57 MET cc_start: 0.8737 (tpt) cc_final: 0.8253 (tpt) REVERT: K 50 ASP cc_start: 0.8121 (t0) cc_final: 0.7791 (t0) REVERT: K 136 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8422 (mm-30) REVERT: K 140 LEU cc_start: 0.9473 (mp) cc_final: 0.9263 (mm) REVERT: K 154 ASP cc_start: 0.7579 (t0) cc_final: 0.7222 (t0) REVERT: A 138 GLU cc_start: 0.8217 (pp20) cc_final: 0.7949 (pp20) REVERT: A 192 ASN cc_start: 0.8333 (t0) cc_final: 0.7997 (t0) outliers start: 21 outliers final: 9 residues processed: 131 average time/residue: 0.2438 time to fit residues: 50.3483 Evaluate side-chains 117 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 229 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 569 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 84 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 257 GLN E 46 GLN ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15223 Z= 0.212 Angle : 0.577 10.292 20509 Z= 0.297 Chirality : 0.040 0.166 2321 Planarity : 0.004 0.038 2556 Dihedral : 5.605 55.726 1981 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.49 % Allowed : 13.46 % Favored : 85.05 % 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: -0.41 (0.20), residues: 1756 helix: 0.84 (0.18), residues: 862 sheet: -0.89 (0.31), residues: 262 loop : -1.50 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 18 HIS 0.003 0.001 HIS B 209 PHE 0.014 0.001 PHE I 127 TYR 0.016 0.001 TYR B 187 ARG 0.004 0.000 ARG K 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 136 THR cc_start: 0.9282 (p) cc_final: 0.9072 (t) REVERT: H 200 MET cc_start: 0.9037 (mpp) cc_final: 0.8668 (mmm) REVERT: J 48 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7889 (mt-10) REVERT: F 156 GLN cc_start: 0.9292 (mm110) cc_final: 0.9032 (mp10) REVERT: E 47 MET cc_start: 0.8856 (ppp) cc_final: 0.8467 (ppp) REVERT: E 52 MET cc_start: 0.9175 (mtm) cc_final: 0.8961 (mtp) REVERT: E 57 MET cc_start: 0.8665 (tpt) cc_final: 0.7867 (tpp) REVERT: K 50 ASP cc_start: 0.8050 (t0) cc_final: 0.7714 (t0) REVERT: K 136 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8369 (mm-30) REVERT: K 140 LEU cc_start: 0.9418 (mp) cc_final: 0.9191 (mm) REVERT: K 154 ASP cc_start: 0.7533 (t0) cc_final: 0.7309 (t0) REVERT: A 138 GLU cc_start: 0.8246 (pp20) cc_final: 0.7952 (pp20) REVERT: A 192 ASN cc_start: 0.8357 (t0) cc_final: 0.8037 (t0) REVERT: B 362 TRP cc_start: 0.8772 (m100) cc_final: 0.8531 (m100) REVERT: B 521 MET cc_start: 0.8979 (mmp) cc_final: 0.8551 (mmp) REVERT: B 523 LEU cc_start: 0.9448 (tp) cc_final: 0.9183 (tt) outliers start: 25 outliers final: 8 residues processed: 139 average time/residue: 0.2311 time to fit residues: 51.4575 Evaluate side-chains 116 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 229 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 156 MET Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN B 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 15223 Z= 0.269 Angle : 0.598 10.229 20509 Z= 0.310 Chirality : 0.041 0.180 2321 Planarity : 0.004 0.040 2556 Dihedral : 5.533 57.033 1981 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.97 % Allowed : 14.89 % Favored : 83.14 % 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: -0.35 (0.20), residues: 1756 helix: 0.91 (0.18), residues: 860 sheet: -0.73 (0.31), residues: 259 loop : -1.56 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 457 HIS 0.004 0.001 HIS B 188 PHE 0.020 0.001 PHE I 127 TYR 0.014 0.001 TYR B 187 ARG 0.003 0.000 ARG K 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 136 THR cc_start: 0.9300 (p) cc_final: 0.9087 (t) REVERT: H 200 MET cc_start: 0.9003 (mpp) cc_final: 0.8685 (mmm) REVERT: H 214 MET cc_start: 0.9133 (mmm) cc_final: 0.8915 (tpt) REVERT: J 48 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7955 (mt-10) REVERT: J 193 ASN cc_start: 0.8699 (t0) cc_final: 0.8443 (t0) REVERT: F 156 GLN cc_start: 0.9319 (mm110) cc_final: 0.9036 (mp10) REVERT: E 47 MET cc_start: 0.8817 (ppp) cc_final: 0.8317 (ppp) REVERT: E 52 MET cc_start: 0.9191 (mtm) cc_final: 0.8979 (mtp) REVERT: E 57 MET cc_start: 0.8799 (tpt) cc_final: 0.8020 (tpp) REVERT: E 93 HIS cc_start: 0.8265 (OUTLIER) cc_final: 0.7702 (m90) REVERT: K 50 ASP cc_start: 0.8154 (t0) cc_final: 0.7764 (t0) REVERT: K 140 LEU cc_start: 0.9434 (mp) cc_final: 0.9205 (mm) REVERT: K 154 ASP cc_start: 0.7652 (t0) cc_final: 0.7430 (t0) REVERT: A 138 GLU cc_start: 0.8253 (pp20) cc_final: 0.7971 (pp20) REVERT: A 192 ASN cc_start: 0.8427 (t0) cc_final: 0.8069 (t0) REVERT: B 249 MET cc_start: 0.5561 (ptm) cc_final: 0.5358 (tmm) REVERT: B 351 MET cc_start: 0.8290 (ppp) cc_final: 0.8020 (ppp) REVERT: B 521 MET cc_start: 0.8934 (mmp) cc_final: 0.8621 (mmp) outliers start: 33 outliers final: 18 residues processed: 138 average time/residue: 0.2397 time to fit residues: 52.7778 Evaluate side-chains 128 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 0.0040 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 15223 Z= 0.273 Angle : 0.596 10.186 20509 Z= 0.307 Chirality : 0.041 0.170 2321 Planarity : 0.004 0.042 2556 Dihedral : 5.512 59.579 1981 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.85 % Allowed : 16.14 % Favored : 82.01 % 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: -0.28 (0.20), residues: 1756 helix: 0.94 (0.18), residues: 859 sheet: -0.66 (0.31), residues: 259 loop : -1.49 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 162 HIS 0.004 0.001 HIS B 188 PHE 0.019 0.001 PHE I 127 TYR 0.013 0.001 TYR B 187 ARG 0.003 0.000 ARG J 172 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 191 MET cc_start: 0.7303 (mmm) cc_final: 0.6814 (mmm) REVERT: H 200 MET cc_start: 0.9109 (mpp) cc_final: 0.8827 (mmm) REVERT: H 220 GLN cc_start: 0.7742 (tt0) cc_final: 0.7350 (tt0) REVERT: J 193 ASN cc_start: 0.8704 (t0) cc_final: 0.8445 (t0) REVERT: F 156 GLN cc_start: 0.9309 (mm110) cc_final: 0.9044 (mp10) REVERT: E 47 MET cc_start: 0.8812 (ppp) cc_final: 0.8318 (ppp) REVERT: E 52 MET cc_start: 0.9205 (mtm) cc_final: 0.8983 (mtp) REVERT: E 57 MET cc_start: 0.8812 (tpt) cc_final: 0.8032 (tpp) REVERT: K 50 ASP cc_start: 0.8170 (t0) cc_final: 0.7868 (t0) REVERT: K 140 LEU cc_start: 0.9452 (mp) cc_final: 0.9245 (mm) REVERT: K 154 ASP cc_start: 0.7752 (t0) cc_final: 0.7517 (t0) REVERT: A 138 GLU cc_start: 0.8274 (pp20) cc_final: 0.7980 (pp20) REVERT: A 192 ASN cc_start: 0.8456 (t0) cc_final: 0.8084 (t0) REVERT: B 249 MET cc_start: 0.5702 (ptm) cc_final: 0.5156 (tmm) REVERT: B 351 MET cc_start: 0.8357 (ppp) cc_final: 0.7796 (ppp) REVERT: B 521 MET cc_start: 0.8884 (mmp) cc_final: 0.8561 (mmp) outliers start: 31 outliers final: 21 residues processed: 133 average time/residue: 0.2591 time to fit residues: 55.8637 Evaluate side-chains 126 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 99 optimal weight: 0.4980 chunk 127 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 146 optimal weight: 0.0980 chunk 97 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 15223 Z= 0.286 Angle : 0.618 11.393 20509 Z= 0.315 Chirality : 0.041 0.165 2321 Planarity : 0.004 0.051 2556 Dihedral : 5.528 59.620 1981 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.61 % Allowed : 16.91 % Favored : 81.48 % 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: -0.28 (0.20), residues: 1756 helix: 0.98 (0.18), residues: 853 sheet: -0.61 (0.32), residues: 251 loop : -1.55 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 162 HIS 0.004 0.001 HIS B 188 PHE 0.019 0.001 PHE I 127 TYR 0.013 0.001 TYR B 187 ARG 0.003 0.000 ARG J 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 200 MET cc_start: 0.9163 (mpp) cc_final: 0.8871 (mmm) REVERT: H 220 GLN cc_start: 0.7752 (tt0) cc_final: 0.7349 (tt0) REVERT: J 193 ASN cc_start: 0.8732 (t0) cc_final: 0.8449 (t0) REVERT: F 156 GLN cc_start: 0.9297 (mm110) cc_final: 0.9046 (mp10) REVERT: E 47 MET cc_start: 0.8805 (ppp) cc_final: 0.8305 (ppp) REVERT: E 52 MET cc_start: 0.9189 (mtm) cc_final: 0.8827 (mtp) REVERT: E 57 MET cc_start: 0.8826 (tpt) cc_final: 0.8044 (tpp) REVERT: K 50 ASP cc_start: 0.8178 (t0) cc_final: 0.7864 (t0) REVERT: K 140 LEU cc_start: 0.9474 (mp) cc_final: 0.9258 (mm) REVERT: K 154 ASP cc_start: 0.7679 (t0) cc_final: 0.7469 (t0) REVERT: A 138 GLU cc_start: 0.8185 (pp20) cc_final: 0.7874 (pp20) REVERT: A 192 ASN cc_start: 0.8499 (t0) cc_final: 0.8106 (t0) REVERT: B 249 MET cc_start: 0.5633 (ptm) cc_final: 0.5344 (tmm) REVERT: B 351 MET cc_start: 0.8556 (ppp) cc_final: 0.8219 (ppp) REVERT: B 521 MET cc_start: 0.8870 (mmp) cc_final: 0.8551 (mmp) outliers start: 27 outliers final: 20 residues processed: 130 average time/residue: 0.2397 time to fit residues: 49.8011 Evaluate side-chains 125 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 65 ASN J 243 ASN B 559 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15223 Z= 0.228 Angle : 0.598 10.272 20509 Z= 0.302 Chirality : 0.040 0.164 2321 Planarity : 0.004 0.058 2556 Dihedral : 5.417 58.904 1981 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.55 % Allowed : 17.69 % Favored : 80.76 % 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: -0.14 (0.21), residues: 1756 helix: 1.07 (0.18), residues: 860 sheet: -0.54 (0.32), residues: 251 loop : -1.48 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 162 HIS 0.003 0.001 HIS B 188 PHE 0.015 0.001 PHE I 127 TYR 0.014 0.001 TYR B 187 ARG 0.002 0.000 ARG B 626 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 1.821 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: H 200 MET cc_start: 0.9102 (mpp) cc_final: 0.8849 (mmm) REVERT: H 220 GLN cc_start: 0.7741 (tt0) cc_final: 0.7048 (tt0) REVERT: J 193 ASN cc_start: 0.8735 (t0) cc_final: 0.8458 (t0) REVERT: F 156 GLN cc_start: 0.9238 (mm110) cc_final: 0.9028 (mp10) REVERT: E 47 MET cc_start: 0.8733 (ppp) cc_final: 0.8267 (ppp) REVERT: E 52 MET cc_start: 0.9186 (mtm) cc_final: 0.8934 (mtp) REVERT: E 57 MET cc_start: 0.8768 (tpt) cc_final: 0.7967 (tpp) REVERT: K 50 ASP cc_start: 0.8189 (t0) cc_final: 0.7875 (t0) REVERT: K 113 MET cc_start: 0.8487 (ppp) cc_final: 0.7680 (ppp) REVERT: K 140 LEU cc_start: 0.9453 (mp) cc_final: 0.9247 (mm) REVERT: K 154 ASP cc_start: 0.7762 (t0) cc_final: 0.7522 (t0) REVERT: A 71 ARG cc_start: 0.8915 (pmt-80) cc_final: 0.8608 (pmt-80) REVERT: A 138 GLU cc_start: 0.8172 (pp20) cc_final: 0.7850 (pp20) REVERT: A 192 ASN cc_start: 0.8502 (t0) cc_final: 0.8122 (t0) REVERT: B 249 MET cc_start: 0.5782 (ptm) cc_final: 0.5500 (tmm) REVERT: B 351 MET cc_start: 0.8528 (ppp) cc_final: 0.8291 (ppp) REVERT: B 362 TRP cc_start: 0.8804 (m100) cc_final: 0.8528 (m100) REVERT: B 521 MET cc_start: 0.8929 (mmp) cc_final: 0.8685 (mmp) outliers start: 26 outliers final: 21 residues processed: 136 average time/residue: 0.2679 time to fit residues: 56.3871 Evaluate side-chains 129 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain K residue 85 ASP Chi-restraints excluded: chain K residue 144 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.0070 chunk 151 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN B 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 15223 Z= 0.183 Angle : 0.592 12.330 20509 Z= 0.296 Chirality : 0.041 0.289 2321 Planarity : 0.004 0.058 2556 Dihedral : 5.261 58.951 1981 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.13 % Allowed : 18.28 % Favored : 80.58 % 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: 0.02 (0.21), residues: 1756 helix: 1.25 (0.19), residues: 857 sheet: -0.52 (0.32), residues: 245 loop : -1.42 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 457 HIS 0.003 0.001 HIS B 188 PHE 0.011 0.001 PHE I 49 TYR 0.014 0.001 TYR B 187 ARG 0.003 0.000 ARG I 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.994 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: H 136 THR cc_start: 0.9321 (p) cc_final: 0.9099 (t) REVERT: H 220 GLN cc_start: 0.7703 (tt0) cc_final: 0.7338 (tt0) REVERT: J 62 MET cc_start: 0.8512 (tpp) cc_final: 0.8300 (tpp) REVERT: J 193 ASN cc_start: 0.8721 (t0) cc_final: 0.8459 (t0) REVERT: E 47 MET cc_start: 0.8739 (ppp) cc_final: 0.8351 (ppp) REVERT: E 52 MET cc_start: 0.9185 (mtm) cc_final: 0.8951 (mtp) REVERT: E 57 MET cc_start: 0.8786 (tpt) cc_final: 0.7980 (tpp) REVERT: K 50 ASP cc_start: 0.8109 (t0) cc_final: 0.7814 (t0) REVERT: K 113 MET cc_start: 0.8498 (ppp) cc_final: 0.7678 (ppp) REVERT: A 71 ARG cc_start: 0.8891 (pmt-80) cc_final: 0.8685 (pmt-80) REVERT: A 138 GLU cc_start: 0.8195 (pp20) cc_final: 0.7869 (pp20) REVERT: A 192 ASN cc_start: 0.8340 (t0) cc_final: 0.7960 (t0) REVERT: B 249 MET cc_start: 0.5641 (ptm) cc_final: 0.5382 (tmm) REVERT: B 351 MET cc_start: 0.8522 (ppp) cc_final: 0.8296 (ppp) REVERT: B 362 TRP cc_start: 0.8794 (m100) cc_final: 0.8498 (m100) REVERT: B 521 MET cc_start: 0.8834 (mmp) cc_final: 0.8627 (mmp) outliers start: 19 outliers final: 17 residues processed: 133 average time/residue: 0.2580 time to fit residues: 53.6841 Evaluate side-chains 127 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 165 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 113 optimal weight: 0.0570 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15223 Z= 0.195 Angle : 0.629 14.610 20509 Z= 0.307 Chirality : 0.041 0.359 2321 Planarity : 0.004 0.059 2556 Dihedral : 5.237 59.025 1981 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.43 % Allowed : 18.40 % Favored : 80.17 % 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: 0.03 (0.21), residues: 1756 helix: 1.29 (0.18), residues: 852 sheet: -0.50 (0.32), residues: 245 loop : -1.45 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 457 HIS 0.004 0.001 HIS K 172 PHE 0.011 0.001 PHE I 127 TYR 0.014 0.001 TYR B 187 ARG 0.004 0.000 ARG K 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3512 Ramachandran restraints generated. 1756 Oldfield, 0 Emsley, 1756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 2.092 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: H 136 THR cc_start: 0.9307 (p) cc_final: 0.9066 (t) REVERT: H 220 GLN cc_start: 0.7719 (tt0) cc_final: 0.7334 (tt0) REVERT: J 62 MET cc_start: 0.8516 (tpp) cc_final: 0.8308 (tpp) REVERT: J 193 ASN cc_start: 0.8718 (t0) cc_final: 0.8458 (t0) REVERT: E 47 MET cc_start: 0.8751 (ppp) cc_final: 0.8362 (ppp) REVERT: E 52 MET cc_start: 0.9185 (mtm) cc_final: 0.8957 (mtp) REVERT: E 57 MET cc_start: 0.8797 (tpt) cc_final: 0.7987 (tpp) REVERT: E 93 HIS cc_start: 0.8256 (OUTLIER) cc_final: 0.7666 (m90) REVERT: K 50 ASP cc_start: 0.8126 (t0) cc_final: 0.7822 (t0) REVERT: K 113 MET cc_start: 0.8365 (ppp) cc_final: 0.7587 (ppp) REVERT: A 138 GLU cc_start: 0.8196 (pp20) cc_final: 0.7863 (pp20) REVERT: A 192 ASN cc_start: 0.8172 (t0) cc_final: 0.7840 (t0) REVERT: B 249 MET cc_start: 0.5695 (ptm) cc_final: 0.5394 (tmm) REVERT: B 351 MET cc_start: 0.8539 (ppp) cc_final: 0.8299 (ppp) REVERT: B 362 TRP cc_start: 0.8814 (m100) cc_final: 0.8513 (m100) REVERT: B 521 MET cc_start: 0.8822 (mmp) cc_final: 0.8615 (mmp) outliers start: 24 outliers final: 21 residues processed: 131 average time/residue: 0.2432 time to fit residues: 50.8487 Evaluate side-chains 133 residues out of total 1680 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 154 MET Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 474 MET Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 131 optimal weight: 0.0570 chunk 21 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 3.9990 chunk 59 optimal weight: 0.0770 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.043042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.034123 restraints weight = 96080.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.035373 restraints weight = 48344.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036222 restraints weight = 30518.619| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15223 Z= 0.172 Angle : 0.620 13.166 20509 Z= 0.303 Chirality : 0.041 0.362 2321 Planarity : 0.004 0.058 2556 Dihedral : 5.132 59.377 1981 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.19 % Allowed : 18.64 % Favored : 80.17 % 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: 0.12 (0.21), residues: 1756 helix: 1.36 (0.19), residues: 849 sheet: -0.28 (0.34), residues: 222 loop : -1.45 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 457 HIS 0.004 0.001 HIS B 209 PHE 0.012 0.001 PHE I 49 TYR 0.019 0.001 TYR B 437 ARG 0.004 0.000 ARG A 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2677.30 seconds wall clock time: 52 minutes 32.40 seconds (3152.40 seconds total)