Starting phenix.real_space_refine on Fri Jul 3 16:35:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kmt_22928/07_2026/7kmt_22928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kmt_22928/07_2026/7kmt_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 { model { file = "/net/cci-nas-00/data/ceres_data/7kmt_22928/07_2026/7kmt_22928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kmt_22928/07_2026/7kmt_22928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kmt_22928/07_2026/7kmt_22928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kmt_22928/07_2026/7kmt_22928.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kmt_22928/07_2026/7kmt_22928.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kmt_22928/07_2026/7kmt_22928.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 107 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 2.49, per 1000 atoms: 0.17 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 - 3.00 Amino acid : True - 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: 1.06 Conformation dependent library (CDL) restraints added in 447.7 milliseconds 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... Secondary structure from input PDB file: 73 helices and 9 sheets defined 52.7% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'H' and resid 29 through 50 removed outlier: 3.868A pdb=" N GLN H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 190 Processing helix chain 'H' and resid 204 through 220 removed outlier: 3.687A pdb=" N ASP H 208 " --> pdb=" O SER H 204 " (cutoff:3.500A) 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 79 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 161 through 165 Processing helix chain 'J' and resid 175 through 186 Processing helix chain 'J' and resid 186 through 192 Processing helix chain 'J' and resid 226 through 229 Processing helix chain 'J' and resid 230 through 245 removed outlier: 4.111A pdb=" N ALA J 244 " --> pdb=" O PHE J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 281 removed outlier: 3.577A pdb=" N LEU J 275 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 58 removed outlier: 4.754A pdb=" N ASP G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 110 Processing helix chain 'G' and resid 110 through 115 Processing helix chain 'G' and resid 128 through 133 removed outlier: 4.328A pdb=" N ARG G 133 " --> pdb=" O GLU G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 154 Processing helix chain 'G' and resid 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'I' and resid 10 through 21 Processing helix chain 'I' and resid 27 through 45 Processing helix chain 'I' and resid 48 through 76 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 82 through 98 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 109 through 112 Processing helix chain 'I' and resid 122 through 126 removed outlier: 3.626A pdb=" N ASP I 126 " --> pdb=" O PRO I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 137 removed outlier: 4.386A pdb=" N LYS I 136 " --> pdb=" O ASP I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 154 removed outlier: 3.834A pdb=" N LEU I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 170 Processing helix chain 'F' and resid 10 through 21 Processing helix chain 'F' and resid 26 through 45 removed outlier: 3.908A pdb=" N ASP F 44 " --> pdb=" O GLN F 40 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR F 45 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.614A pdb=" N VAL F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) 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 82 through 93 removed outlier: 3.643A pdb=" N THR F 86 " --> pdb=" O ASN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 99 Processing helix chain 'F' and resid 109 through 112 Processing helix chain 'F' and resid 131 through 136 removed outlier: 3.756A pdb=" N LYS F 136 " --> pdb=" O MET F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 removed outlier: 3.748A pdb=" N CYS F 145 " --> pdb=" O SER F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 170 Processing helix chain 'E' and resid 42 through 63 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 101 through 111 Processing helix chain 'E' and resid 112 through 132 Processing helix chain 'E' and resid 158 through 163 removed outlier: 4.004A pdb=" N ASP E 163 " --> pdb=" O PHE E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 169 Processing helix chain 'E' and resid 203 through 212 Processing helix chain 'E' and resid 215 through 227 Processing helix chain 'K' and resid 33 through 53 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) removed outlier: 3.886A pdb=" N TRP K 53 " --> pdb=" O GLU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 146 Processing helix chain 'K' and resid 158 through 173 removed outlier: 3.500A pdb=" N ASP K 162 " --> pdb=" O SER K 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 29 removed outlier: 4.065A pdb=" N LEU A 24 " --> pdb=" O GLY A 20 " (cutoff:3.500A) 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 69 through 77 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 110 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 133 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 157 through 174 removed outlier: 3.521A pdb=" N ALA A 161 " --> pdb=" O ASN A 157 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 174 " --> pdb=" O LYS A 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 25 through 35 removed outlier: 3.752A pdb=" N ARG B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.751A pdb=" N LEU B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 173 removed outlier: 3.671A pdb=" N LEU B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 196 Processing helix chain 'B' and resid 205 through 208 removed outlier: 3.925A pdb=" N ASN B 208 " --> pdb=" O GLU B 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 224 through 236 removed outlier: 3.653A pdb=" N ALA B 228 " --> pdb=" O VAL B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 284 Processing helix chain 'B' and resid 315 through 323 removed outlier: 3.970A pdb=" N ILE B 319 " --> pdb=" O SER B 315 " (cutoff:3.500A) 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) Processing helix chain 'B' and resid 332 through 350 Processing helix chain 'B' and resid 351 through 365 Processing helix chain 'B' and resid 414 through 427 removed outlier: 4.008A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 440 Processing helix chain 'B' and resid 449 through 465 Processing helix chain 'B' and resid 471 through 478 removed outlier: 3.707A pdb=" N ILE B 475 " --> pdb=" O THR B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 497 Processing helix chain 'B' and resid 518 through 530 removed outlier: 3.947A pdb=" N GLU B 526 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 550 removed outlier: 3.532A pdb=" N SER B 537 " --> pdb=" O ASN B 533 " (cutoff:3.500A) Proline residue: B 539 - end of helix removed outlier: 3.622A pdb=" N ASP B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 571 removed outlier: 3.905A pdb=" N MET B 561 " --> pdb=" O CYS B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 636 Processing helix chain 'B' and resid 638 through 655 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) removed outlier: 4.596A pdb=" N GLU B 655 " --> pdb=" O SER B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 673 Processing sheet with id=AA1, first strand: chain 'H' and resid 15 through 20 removed outlier: 3.639A pdb=" N TYR H 17 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 5 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ARG H 120 " --> pdb=" O ILE H 131 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N SER G 71 " --> pdb=" O ARG H 120 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU H 122 " --> pdb=" O SER G 69 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER G 69 " --> pdb=" O LEU H 122 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR H 124 " --> pdb=" O ILE G 67 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE G 67 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ARG G 68 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N PHE G 6 " --> pdb=" O ASP G 18 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP G 18 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE G 8 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ASN G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 56 through 58 Processing sheet with id=AA3, first strand: chain 'J' and resid 251 through 254 removed outlier: 3.821A pdb=" N VAL J 212 " --> pdb=" O ASP J 198 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP J 198 " --> pdb=" O VAL J 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 104 through 105 removed outlier: 6.468A pdb=" N GLU I 175 " --> pdb=" O VAL I 164 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ASP I 158 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.264A pdb=" N GLU F 175 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP F 158 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 175 through 177 Processing sheet with id=AA7, first strand: chain 'K' and resid 14 through 18 removed outlier: 6.145A pdb=" N ALA K 102 " --> pdb=" O LYS K 91 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LYS K 91 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 44 through 52 removed outlier: 3.609A pdb=" N TYR A 7 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 84 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL A 119 " --> pdb=" O ILE A 84 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE A 86 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN A 121 " --> pdb=" O ILE A 86 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR A 88 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 69 through 70 removed outlier: 5.908A pdb=" N ILE B 39 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N VAL B 38 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N SER B 213 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N THR B 40 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ILE B 215 " --> pdb=" O THR B 40 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE B 211 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N VAL B 257 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER B 213 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B 259 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE B 215 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N CYS B 261 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU B 217 " --> pdb=" O CYS B 261 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU B 287 " --> pdb=" O PRO B 256 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2157 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: 2.04 Time building geometry restraints manager: 1.34 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: 0.00 - 2.30: 20060 2.30 - 4.60: 391 4.60 - 6.90: 52 6.90 - 9.19: 5 9.19 - 11.49: 1 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: 173 2.59 - 3.17: 13531 3.17 - 3.75: 23267 3.75 - 4.32: 31711 4.32 - 4.90: 52441 Nonbonded interactions: 121123 Sorted by model distance: nonbonded pdb=" O VAL F 84 " pdb=" OG SER F 87 " model vdw 2.018 3.040 nonbonded pdb=" OG1 THR G 141 " pdb=" OE1 GLU E 200 " model vdw 2.088 3.040 nonbonded pdb=" OE2 GLU B 25 " pdb=" OG SER B 530 " model vdw 2.101 3.040 nonbonded pdb=" OG SER I 165 " pdb=" O GLN I 173 " model vdw 2.105 3.040 nonbonded pdb=" O LEU F 83 " pdb=" OG1 THR F 86 " model vdw 2.123 3.040 ... (remaining 121118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.310 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 11.020 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 15225 Z= 0.221 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 : 7.25 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.015 0.001 ARG K 157 TYR 0.028 0.002 TYR F 57 PHE 0.030 0.002 PHE E 242 TRP 0.017 0.002 TRP B 535 HIS 0.007 0.001 HIS E 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (15223) covalent geometry : angle 0.78985 / 0.43 (20509) hydrogen bonds : bond 0.13705 / 9.21 ( 750) hydrogen bonds : angle 6.89019 / 4.83 ( 2157) Misc. bond : bond 0.02963 / 1.50 ( 2) *********************** 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 to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.623 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: 0.7888 (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: 0.8714 (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: 0.1316 time to fit residues: 39.1929 Evaluate side-chains 123 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 56 GLN G 130 ASN I 181 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 477 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.042445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.033077 restraints weight = 99136.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.034307 restraints weight = 50604.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.035145 restraints weight = 32238.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.035728 restraints weight = 23533.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036131 restraints weight = 18787.146| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 15225 Z= 0.227 Angle : 0.696 14.172 20509 Z= 0.361 Chirality : 0.044 0.166 2321 Planarity : 0.004 0.049 2556 Dihedral : 6.199 58.989 1981 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.66 % Allowed : 8.87 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1756 helix: 0.72 (0.18), residues: 870 sheet: -1.37 (0.30), residues: 264 loop : -1.48 (0.26), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 157 TYR 0.022 0.002 TYR F 57 PHE 0.024 0.002 PHE B 270 TRP 0.015 0.002 TRP F 162 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.23 (15223) covalent geometry : angle 0.69557 / 0.36 (20509) hydrogen bonds : bond 0.04762 / 3.07 ( 750) hydrogen bonds : angle 5.44617 / 3.79 ( 2157) Misc. bond : bond 0.00084 / 0.04 ( 2) *********************** 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 149 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 136 THR cc_start: 0.9396 (p) cc_final: 0.9155 (t) REVERT: H 214 MET cc_start: 0.9346 (tpp) cc_final: 0.9142 (mmm) REVERT: H 220 GLN cc_start: 0.7745 (tt0) cc_final: 0.7206 (tt0) REVERT: J 48 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7812 (mt-10) REVERT: G 36 GLN cc_start: 0.9528 (mp10) cc_final: 0.9207 (mp10) REVERT: G 64 LYS cc_start: 0.8650 (tttt) cc_final: 0.8320 (tttp) REVERT: F 156 GLN cc_start: 0.9252 (mm110) cc_final: 0.8762 (mt0) REVERT: E 47 MET cc_start: 0.9104 (ppp) cc_final: 0.8779 (ppp) REVERT: E 52 MET cc_start: 0.9546 (mtm) cc_final: 0.9018 (mtp) REVERT: E 57 MET cc_start: 0.8859 (tpt) cc_final: 0.8091 (tpp) REVERT: K 49 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8895 (mt-10) REVERT: K 50 ASP cc_start: 0.8606 (t0) cc_final: 0.8251 (t0) REVERT: K 113 MET cc_start: 0.8448 (ppp) cc_final: 0.8079 (ppp) REVERT: K 127 ASP cc_start: 0.8805 (p0) cc_final: 0.8432 (p0) REVERT: K 136 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8606 (mm-30) REVERT: K 140 LEU cc_start: 0.9444 (mp) cc_final: 0.9208 (mm) REVERT: K 154 ASP cc_start: 0.7864 (t0) cc_final: 0.7529 (t0) REVERT: K 171 LYS cc_start: 0.9431 (mttm) cc_final: 0.9032 (mttm) REVERT: A 145 MET cc_start: 0.8892 (tpp) cc_final: 0.8685 (tpp) REVERT: A 192 ASN cc_start: 0.8530 (t0) cc_final: 0.8059 (t0) REVERT: B 261 CYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8732 (t) REVERT: B 343 LEU cc_start: 0.9489 (mt) cc_final: 0.9225 (mt) REVERT: B 351 MET cc_start: 0.8575 (tmm) cc_final: 0.8239 (tmm) REVERT: B 464 MET cc_start: 0.9076 (mmm) cc_final: 0.8789 (tpp) REVERT: B 484 GLU cc_start: 0.8854 (tp30) cc_final: 0.8436 (tp30) outliers start: 11 outliers final: 6 residues processed: 144 average time/residue: 0.1175 time to fit residues: 26.1592 Evaluate side-chains 120 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 113 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 569 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 158 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 257 GLN G 33 ASN G 130 ASN F 55 HIS ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN K 128 ASN A 93 GLN B 76 GLN B 209 HIS B 310 GLN B 641 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.042373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.033067 restraints weight = 99590.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.034305 restraints weight = 49966.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035140 restraints weight = 31864.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.035717 restraints weight = 23299.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.036093 restraints weight = 18613.770| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15225 Z= 0.172 Angle : 0.608 12.967 20509 Z= 0.316 Chirality : 0.042 0.185 2321 Planarity : 0.004 0.042 2556 Dihedral : 5.817 58.813 1981 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.31 % Allowed : 12.33 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.20), residues: 1756 helix: 0.90 (0.18), residues: 874 sheet: -1.20 (0.30), residues: 266 loop : -1.36 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 157 TYR 0.017 0.001 TYR B 187 PHE 0.017 0.001 PHE I 127 TRP 0.013 0.001 TRP F 162 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (15223) covalent geometry : angle 0.60762 / 0.32 (20509) hydrogen bonds : bond 0.04185 / 2.68 ( 750) hydrogen bonds : angle 5.05677 / 3.52 ( 2157) Misc. bond : bond 0.00039 / 0.02 ( 2) *********************** 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 147 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 44 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8692 (t80) REVERT: H 138 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8446 (tp) REVERT: H 200 MET cc_start: 0.9127 (mpp) cc_final: 0.8622 (mmm) REVERT: H 214 MET cc_start: 0.9392 (tpp) cc_final: 0.9117 (mmm) REVERT: H 220 GLN cc_start: 0.7790 (tt0) cc_final: 0.7534 (tt0) REVERT: J 48 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7782 (mt-10) REVERT: G 64 LYS cc_start: 0.8643 (tttt) cc_final: 0.8365 (tttp) REVERT: G 130 ASN cc_start: 0.9337 (OUTLIER) cc_final: 0.8791 (m-40) REVERT: F 156 GLN cc_start: 0.9239 (mm110) cc_final: 0.8866 (mt0) REVERT: E 47 MET cc_start: 0.9055 (ppp) cc_final: 0.8630 (ppp) REVERT: E 52 MET cc_start: 0.9519 (mtm) cc_final: 0.9098 (mtp) REVERT: E 57 MET cc_start: 0.8863 (tpt) cc_final: 0.8052 (tpp) REVERT: K 50 ASP cc_start: 0.8617 (t0) cc_final: 0.8321 (t0) REVERT: K 113 MET cc_start: 0.8381 (ppp) cc_final: 0.8089 (ppp) REVERT: K 136 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8608 (mm-30) REVERT: K 140 LEU cc_start: 0.9413 (mp) cc_final: 0.9201 (mm) REVERT: K 150 TYR cc_start: 0.8600 (t80) cc_final: 0.8395 (t80) REVERT: K 154 ASP cc_start: 0.7897 (t0) cc_final: 0.7496 (t0) REVERT: K 171 LYS cc_start: 0.9408 (mttm) cc_final: 0.9027 (mttm) REVERT: A 173 MET cc_start: 0.8544 (mmm) cc_final: 0.8326 (mmm) REVERT: A 192 ASN cc_start: 0.8577 (t0) cc_final: 0.8115 (t0) REVERT: B 343 LEU cc_start: 0.9490 (mt) cc_final: 0.9222 (mt) REVERT: B 351 MET cc_start: 0.8630 (tmm) cc_final: 0.8215 (tmm) REVERT: B 464 MET cc_start: 0.9083 (mmm) cc_final: 0.8865 (tpp) REVERT: B 484 GLU cc_start: 0.8850 (tp30) cc_final: 0.8380 (tp30) REVERT: B 491 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8836 (mm-30) REVERT: B 521 MET cc_start: 0.9337 (mmp) cc_final: 0.8690 (mmp) outliers start: 22 outliers final: 6 residues processed: 141 average time/residue: 0.1072 time to fit residues: 24.0543 Evaluate side-chains 122 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 130 ASN Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 548 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 48 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 161 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN K 42 HIS K 52 GLN K 129 ASN B 559 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.041250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.032003 restraints weight = 100377.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.033175 restraints weight = 51199.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.033979 restraints weight = 32925.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034522 restraints weight = 24285.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.034911 restraints weight = 19616.848| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 15225 Z= 0.261 Angle : 0.667 13.811 20509 Z= 0.348 Chirality : 0.043 0.165 2321 Planarity : 0.004 0.040 2556 Dihedral : 5.791 58.909 1981 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.14 % Allowed : 13.22 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.20), residues: 1756 helix: 0.87 (0.18), residues: 874 sheet: -1.08 (0.30), residues: 263 loop : -1.46 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 180 TYR 0.016 0.002 TYR B 5 PHE 0.024 0.002 PHE I 127 TRP 0.013 0.001 TRP F 162 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.26 (15223) covalent geometry : angle 0.66737 / 0.35 (20509) hydrogen bonds : bond 0.04330 / 2.79 ( 750) hydrogen bonds : angle 5.15627 / 3.59 ( 2157) Misc. bond : bond 0.00061 / 0.03 ( 2) *********************** 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 154 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 44 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8700 (t80) REVERT: H 191 MET cc_start: 0.7940 (mmm) cc_final: 0.7640 (mmm) REVERT: H 200 MET cc_start: 0.9108 (mpp) cc_final: 0.8538 (mmm) REVERT: H 214 MET cc_start: 0.9410 (tpp) cc_final: 0.9107 (mmm) REVERT: J 48 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7872 (mt-10) REVERT: G 36 GLN cc_start: 0.9507 (mp10) cc_final: 0.8986 (mp10) REVERT: G 39 GLU cc_start: 0.8518 (mp0) cc_final: 0.7449 (pm20) REVERT: G 64 LYS cc_start: 0.8659 (tttt) cc_final: 0.8349 (tttp) REVERT: F 156 GLN cc_start: 0.9252 (mm110) cc_final: 0.8848 (mt0) REVERT: E 47 MET cc_start: 0.8996 (ppp) cc_final: 0.8548 (ppp) REVERT: E 52 MET cc_start: 0.9529 (mtm) cc_final: 0.9230 (mtp) REVERT: E 57 MET cc_start: 0.8966 (tpt) cc_final: 0.8180 (tpp) REVERT: K 50 ASP cc_start: 0.8729 (t0) cc_final: 0.8396 (t0) REVERT: K 113 MET cc_start: 0.8498 (ppp) cc_final: 0.8151 (ppp) REVERT: K 140 LEU cc_start: 0.9455 (mp) cc_final: 0.9231 (mm) REVERT: K 154 ASP cc_start: 0.8021 (t0) cc_final: 0.7779 (t0) REVERT: A 173 MET cc_start: 0.8659 (mmm) cc_final: 0.8441 (mmm) REVERT: A 192 ASN cc_start: 0.8619 (t0) cc_final: 0.8115 (t0) REVERT: B 249 MET cc_start: 0.5579 (ptm) cc_final: 0.5069 (tmm) REVERT: B 261 CYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8936 (t) REVERT: B 343 LEU cc_start: 0.9541 (mt) cc_final: 0.9306 (mt) REVERT: B 351 MET cc_start: 0.8762 (tmm) cc_final: 0.8289 (tmm) REVERT: B 484 GLU cc_start: 0.8880 (tp30) cc_final: 0.8415 (tp30) REVERT: B 491 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8888 (mm-30) REVERT: B 521 MET cc_start: 0.9324 (mmp) cc_final: 0.8674 (mmp) outliers start: 36 outliers final: 17 residues processed: 147 average time/residue: 0.1014 time to fit residues: 24.1892 Evaluate side-chains 129 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 261 CYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 491 GLU 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 569 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 149 optimal weight: 7.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.041193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.032039 restraints weight = 99829.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.033217 restraints weight = 50586.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.034026 restraints weight = 32412.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034573 restraints weight = 23726.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.034962 restraints weight = 19048.449| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 15225 Z= 0.218 Angle : 0.642 13.783 20509 Z= 0.333 Chirality : 0.043 0.183 2321 Planarity : 0.004 0.043 2556 Dihedral : 5.731 58.530 1981 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.97 % Allowed : 15.01 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.20), residues: 1756 helix: 0.91 (0.18), residues: 876 sheet: -1.05 (0.31), residues: 261 loop : -1.37 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 180 TYR 0.015 0.001 TYR B 187 PHE 0.022 0.001 PHE B 415 TRP 0.011 0.001 TRP B 457 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.22 (15223) covalent geometry : angle 0.64202 / 0.33 (20509) hydrogen bonds : bond 0.04199 / 2.70 ( 750) hydrogen bonds : angle 5.05898 / 3.52 ( 2157) Misc. bond : bond 0.00041 / 0.02 ( 2) *********************** 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 151 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.613 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 44 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.8617 (t80) REVERT: H 138 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8537 (tp) REVERT: H 198 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8628 (tpp) REVERT: H 200 MET cc_start: 0.9282 (mpp) cc_final: 0.8815 (mmm) REVERT: H 214 MET cc_start: 0.9388 (tpp) cc_final: 0.9098 (mmm) REVERT: J 48 GLU cc_start: 0.8316 (mt-10) cc_final: 0.7868 (mt-10) REVERT: J 62 MET cc_start: 0.9037 (tpp) cc_final: 0.8758 (tpp) REVERT: G 64 LYS cc_start: 0.8610 (tttt) cc_final: 0.8301 (tttp) REVERT: F 156 GLN cc_start: 0.9247 (mm110) cc_final: 0.8845 (mt0) REVERT: E 47 MET cc_start: 0.8980 (ppp) cc_final: 0.8519 (ppp) REVERT: E 52 MET cc_start: 0.9526 (mtm) cc_final: 0.9229 (mtp) REVERT: E 57 MET cc_start: 0.9004 (tpt) cc_final: 0.8230 (tpp) REVERT: K 50 ASP cc_start: 0.8730 (t0) cc_final: 0.8375 (t0) REVERT: K 113 MET cc_start: 0.8486 (ppp) cc_final: 0.8155 (ppp) REVERT: K 136 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8510 (mm-30) REVERT: K 140 LEU cc_start: 0.9445 (mp) cc_final: 0.9218 (mm) REVERT: K 154 ASP cc_start: 0.8078 (t0) cc_final: 0.7820 (t0) REVERT: A 192 ASN cc_start: 0.8627 (t0) cc_final: 0.8074 (t0) REVERT: B 249 MET cc_start: 0.5774 (ptm) cc_final: 0.5438 (tmm) REVERT: B 343 LEU cc_start: 0.9530 (mt) cc_final: 0.9294 (mt) REVERT: B 351 MET cc_start: 0.8782 (tmm) cc_final: 0.8291 (tmm) REVERT: B 484 GLU cc_start: 0.8876 (tp30) cc_final: 0.8401 (tp30) REVERT: B 491 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8833 (mm-30) REVERT: B 521 MET cc_start: 0.9288 (mmp) cc_final: 0.8900 (mmp) outliers start: 33 outliers final: 19 residues processed: 142 average time/residue: 0.0938 time to fit residues: 21.6128 Evaluate side-chains 131 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 200 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain I residue 111 ASN Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU 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 491 GLU 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 665 ILE 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 83 optimal weight: 1.9990 chunk 169 optimal weight: 0.1980 chunk 140 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 127 optimal weight: 0.0770 chunk 155 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 120 optimal weight: 0.3980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.042770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.033568 restraints weight = 96968.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.034827 restraints weight = 48840.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.035675 restraints weight = 30837.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036251 restraints weight = 22384.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036664 restraints weight = 17797.204| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15225 Z= 0.115 Angle : 0.592 11.554 20509 Z= 0.303 Chirality : 0.041 0.186 2321 Planarity : 0.004 0.044 2556 Dihedral : 5.510 56.917 1981 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.37 % Allowed : 15.78 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.20), residues: 1756 helix: 1.19 (0.18), residues: 869 sheet: -0.73 (0.31), residues: 251 loop : -1.32 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 254 TYR 0.017 0.001 TYR B 187 PHE 0.012 0.001 PHE H 127 TRP 0.012 0.001 TRP I 18 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (15223) covalent geometry : angle 0.59193 / 0.30 (20509) hydrogen bonds : bond 0.03727 / 2.40 ( 750) hydrogen bonds : angle 4.71557 / 3.27 ( 2157) Misc. bond : bond 0.00013 / 0.01 ( 2) *********************** 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 152 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 198 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8710 (tpp) REVERT: H 200 MET cc_start: 0.9005 (mpp) cc_final: 0.8683 (mmm) REVERT: H 214 MET cc_start: 0.9310 (tpp) cc_final: 0.9110 (tpt) REVERT: J 48 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7783 (mt-10) REVERT: J 62 MET cc_start: 0.9025 (tpp) cc_final: 0.8733 (tpp) REVERT: J 193 ASN cc_start: 0.8910 (t0) cc_final: 0.8628 (t0) REVERT: G 64 LYS cc_start: 0.8533 (tttt) cc_final: 0.8223 (tttp) REVERT: F 135 MET cc_start: 0.8491 (tpt) cc_final: 0.8282 (mmm) REVERT: F 156 GLN cc_start: 0.9209 (mm110) cc_final: 0.8889 (mt0) REVERT: E 47 MET cc_start: 0.8959 (ppp) cc_final: 0.8429 (ppp) REVERT: E 52 MET cc_start: 0.9509 (mtm) cc_final: 0.9219 (mtp) REVERT: K 50 ASP cc_start: 0.8688 (t0) cc_final: 0.8332 (t0) REVERT: K 113 MET cc_start: 0.8238 (ppp) cc_final: 0.7758 (ppp) REVERT: K 136 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8384 (mm-30) REVERT: K 154 ASP cc_start: 0.8008 (t0) cc_final: 0.7785 (t0) REVERT: K 171 LYS cc_start: 0.9388 (mttm) cc_final: 0.9122 (mttm) REVERT: A 192 ASN cc_start: 0.8618 (t0) cc_final: 0.8096 (t0) REVERT: B 249 MET cc_start: 0.5559 (ptm) cc_final: 0.5081 (tmm) REVERT: B 343 LEU cc_start: 0.9490 (mt) cc_final: 0.9271 (mt) REVERT: B 351 MET cc_start: 0.8745 (tmm) cc_final: 0.8254 (tmm) REVERT: B 362 TRP cc_start: 0.9144 (m100) cc_final: 0.8741 (m100) REVERT: B 484 GLU cc_start: 0.8980 (tp30) cc_final: 0.8503 (tp30) REVERT: B 491 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8795 (mm-30) REVERT: B 521 MET cc_start: 0.9226 (mmp) cc_final: 0.8791 (mmp) outliers start: 23 outliers final: 11 residues processed: 145 average time/residue: 0.1127 time to fit residues: 25.1430 Evaluate side-chains 126 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 153 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 132 optimal weight: 0.4980 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 174 optimal weight: 0.0470 chunk 173 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 220 GLN J 184 HIS ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.042910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.033728 restraints weight = 97023.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.034978 restraints weight = 48770.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.035826 restraints weight = 30944.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.036389 restraints weight = 22459.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036810 restraints weight = 17883.422| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15225 Z= 0.113 Angle : 0.593 10.209 20509 Z= 0.301 Chirality : 0.041 0.182 2321 Planarity : 0.004 0.050 2556 Dihedral : 5.378 59.640 1981 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.67 % Allowed : 16.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.21), residues: 1756 helix: 1.30 (0.18), residues: 871 sheet: -0.54 (0.31), residues: 251 loop : -1.31 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 157 TYR 0.016 0.001 TYR B 187 PHE 0.012 0.001 PHE I 49 TRP 0.012 0.001 TRP B 457 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (15223) covalent geometry : angle 0.59303 / 0.30 (20509) hydrogen bonds : bond 0.03606 / 2.33 ( 750) hydrogen bonds : angle 4.65463 / 3.23 ( 2157) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** 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 152 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.625 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 199 GLU cc_start: 0.8567 (mp0) cc_final: 0.8096 (pp20) REVERT: H 200 MET cc_start: 0.8979 (mpp) cc_final: 0.7903 (mpp) REVERT: J 48 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7770 (mt-10) REVERT: J 62 MET cc_start: 0.9042 (tpp) cc_final: 0.8747 (tpp) REVERT: J 193 ASN cc_start: 0.8927 (t0) cc_final: 0.8620 (t0) REVERT: G 40 ASP cc_start: 0.9445 (m-30) cc_final: 0.9178 (m-30) REVERT: G 64 LYS cc_start: 0.8533 (tttt) cc_final: 0.8228 (tttp) REVERT: F 135 MET cc_start: 0.8475 (tpt) cc_final: 0.8272 (mmm) REVERT: F 156 GLN cc_start: 0.9202 (mm110) cc_final: 0.8918 (mt0) REVERT: E 47 MET cc_start: 0.8970 (ppp) cc_final: 0.8583 (ppp) REVERT: E 52 MET cc_start: 0.9518 (mtm) cc_final: 0.9211 (mtp) REVERT: K 50 ASP cc_start: 0.8687 (t0) cc_final: 0.8332 (t0) REVERT: K 113 MET cc_start: 0.8220 (ppp) cc_final: 0.7783 (ppp) REVERT: K 154 ASP cc_start: 0.8098 (t0) cc_final: 0.7828 (t0) REVERT: A 192 ASN cc_start: 0.8632 (t0) cc_final: 0.8129 (t0) REVERT: B 249 MET cc_start: 0.5446 (ptm) cc_final: 0.4980 (tmm) REVERT: B 313 MET cc_start: 0.7798 (mmm) cc_final: 0.6330 (tpp) REVERT: B 351 MET cc_start: 0.8720 (tmm) cc_final: 0.8251 (tmm) REVERT: B 362 TRP cc_start: 0.9178 (m100) cc_final: 0.8725 (m100) REVERT: B 484 GLU cc_start: 0.8951 (tp30) cc_final: 0.8456 (tp30) REVERT: B 491 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8798 (mm-30) REVERT: B 521 MET cc_start: 0.9164 (mmp) cc_final: 0.8801 (mmt) outliers start: 28 outliers final: 16 residues processed: 147 average time/residue: 0.1041 time to fit residues: 24.2700 Evaluate side-chains 129 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain I residue 164 VAL Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 0.0010 chunk 147 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.0570 chunk 128 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 overall best weight: 0.9506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 220 GLN ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.042515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.033509 restraints weight = 96465.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.034717 restraints weight = 48621.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.035549 restraints weight = 30849.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036127 restraints weight = 22329.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.036508 restraints weight = 17638.832| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15225 Z= 0.127 Angle : 0.603 9.850 20509 Z= 0.305 Chirality : 0.041 0.225 2321 Planarity : 0.004 0.049 2556 Dihedral : 5.315 58.009 1981 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.37 % Allowed : 16.91 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.21), residues: 1756 helix: 1.33 (0.18), residues: 876 sheet: -0.53 (0.31), residues: 253 loop : -1.30 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 157 TYR 0.015 0.001 TYR B 187 PHE 0.012 0.001 PHE I 49 TRP 0.012 0.001 TRP B 457 HIS 0.003 0.001 HIS J 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (15223) covalent geometry : angle 0.60307 / 0.30 (20509) hydrogen bonds : bond 0.03598 / 2.32 ( 750) hydrogen bonds : angle 4.65900 / 3.22 ( 2157) Misc. bond : bond 0.00018 / 0.01 ( 2) *********************** 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 145 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 SER cc_start: 0.8807 (m) cc_final: 0.8578 (p) REVERT: H 198 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8425 (tpp) REVERT: H 200 MET cc_start: 0.8983 (mpp) cc_final: 0.8754 (mmm) REVERT: H 220 GLN cc_start: 0.7305 (mt0) cc_final: 0.7101 (mm-40) REVERT: J 48 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7741 (mt-10) REVERT: J 62 MET cc_start: 0.9046 (tpp) cc_final: 0.8737 (tpp) REVERT: J 193 ASN cc_start: 0.8916 (t0) cc_final: 0.8612 (t0) REVERT: G 64 LYS cc_start: 0.8517 (tttt) cc_final: 0.8220 (tttp) REVERT: F 135 MET cc_start: 0.8539 (tpt) cc_final: 0.8281 (mmm) REVERT: F 156 GLN cc_start: 0.9234 (mm110) cc_final: 0.8867 (mt0) REVERT: E 47 MET cc_start: 0.8978 (ppp) cc_final: 0.8719 (ppp) REVERT: E 52 MET cc_start: 0.9512 (mtm) cc_final: 0.9196 (mtp) REVERT: K 50 ASP cc_start: 0.8709 (t0) cc_final: 0.8344 (t0) REVERT: K 113 MET cc_start: 0.8409 (ppp) cc_final: 0.7946 (ppp) REVERT: K 136 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8440 (mm-30) REVERT: K 154 ASP cc_start: 0.8232 (t0) cc_final: 0.7973 (t0) REVERT: A 192 ASN cc_start: 0.8646 (t0) cc_final: 0.8142 (t0) REVERT: B 249 MET cc_start: 0.5525 (ptm) cc_final: 0.5085 (tmm) REVERT: B 351 MET cc_start: 0.8694 (tmm) cc_final: 0.8262 (tmm) REVERT: B 362 TRP cc_start: 0.9195 (m100) cc_final: 0.8772 (m100) REVERT: B 484 GLU cc_start: 0.8964 (tp30) cc_final: 0.8453 (tp30) REVERT: B 491 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8794 (mm-30) REVERT: B 521 MET cc_start: 0.9129 (mmp) cc_final: 0.8776 (mmt) outliers start: 23 outliers final: 16 residues processed: 138 average time/residue: 0.1130 time to fit residues: 24.6599 Evaluate side-chains 131 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 34 optimal weight: 0.0010 chunk 163 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 104 optimal weight: 0.0470 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 0.1980 chunk 31 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 140 optimal weight: 0.3980 overall best weight: 0.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 55 GLN ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.042990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033873 restraints weight = 95981.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.035144 restraints weight = 48328.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.036007 restraints weight = 30385.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036596 restraints weight = 21808.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.036995 restraints weight = 17155.298| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15225 Z= 0.109 Angle : 0.630 10.220 20509 Z= 0.313 Chirality : 0.041 0.190 2321 Planarity : 0.004 0.051 2556 Dihedral : 5.151 59.845 1981 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.01 % Allowed : 17.69 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1756 helix: 1.37 (0.18), residues: 875 sheet: -0.36 (0.32), residues: 253 loop : -1.26 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 71 TYR 0.016 0.001 TYR B 187 PHE 0.012 0.001 PHE I 49 TRP 0.012 0.001 TRP A 102 HIS 0.003 0.001 HIS J 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (15223) covalent geometry : angle 0.63041 / 0.31 (20509) hydrogen bonds : bond 0.03443 / 2.22 ( 750) hydrogen bonds : angle 4.55663 / 3.14 ( 2157) Misc. bond : bond 0.00013 / 0.01 ( 2) *********************** 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 140 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.579 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 198 MET cc_start: 0.8716 (tpt) cc_final: 0.8435 (tpp) REVERT: H 199 GLU cc_start: 0.8299 (pm20) cc_final: 0.7954 (pp20) REVERT: H 200 MET cc_start: 0.8808 (mpp) cc_final: 0.8348 (mmm) REVERT: J 48 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7714 (mt-10) REVERT: J 62 MET cc_start: 0.9106 (tpp) cc_final: 0.8798 (tpp) REVERT: J 193 ASN cc_start: 0.8935 (t0) cc_final: 0.8619 (t0) REVERT: G 64 LYS cc_start: 0.8474 (tttt) cc_final: 0.8143 (tttp) REVERT: F 135 MET cc_start: 0.8659 (tpt) cc_final: 0.8354 (mmm) REVERT: F 156 GLN cc_start: 0.9167 (mm110) cc_final: 0.8903 (mt0) REVERT: E 47 MET cc_start: 0.8922 (ppp) cc_final: 0.8569 (ppp) REVERT: E 52 MET cc_start: 0.9553 (mtm) cc_final: 0.9253 (mtp) REVERT: K 50 ASP cc_start: 0.8749 (t0) cc_final: 0.8180 (t0) REVERT: K 113 MET cc_start: 0.8146 (ppp) cc_final: 0.7707 (ppp) REVERT: K 136 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8575 (mm-30) REVERT: K 154 ASP cc_start: 0.8301 (t0) cc_final: 0.8034 (t0) REVERT: A 145 MET cc_start: 0.8438 (tpp) cc_final: 0.8057 (tpp) REVERT: A 192 ASN cc_start: 0.8578 (t0) cc_final: 0.8117 (t0) REVERT: B 249 MET cc_start: 0.5320 (ptm) cc_final: 0.4918 (tmm) REVERT: B 313 MET cc_start: 0.7984 (mmm) cc_final: 0.6486 (tpp) REVERT: B 351 MET cc_start: 0.8848 (tmm) cc_final: 0.8388 (tmm) REVERT: B 362 TRP cc_start: 0.9191 (m100) cc_final: 0.8766 (m100) REVERT: B 491 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8855 (mm-30) REVERT: B 521 MET cc_start: 0.9119 (mmp) cc_final: 0.8847 (mmt) outliers start: 17 outliers final: 13 residues processed: 135 average time/residue: 0.1117 time to fit residues: 24.1551 Evaluate side-chains 129 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain A residue 70 PHE Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 155 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 220 GLN ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 559 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.042514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.033431 restraints weight = 96833.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.034671 restraints weight = 48752.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.035511 restraints weight = 30852.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.036089 restraints weight = 22262.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036500 restraints weight = 17591.421| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15225 Z= 0.125 Angle : 0.636 14.519 20509 Z= 0.314 Chirality : 0.041 0.302 2321 Planarity : 0.003 0.048 2556 Dihedral : 5.093 58.004 1981 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.07 % Allowed : 17.81 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.21), residues: 1756 helix: 1.42 (0.18), residues: 875 sheet: -0.34 (0.32), residues: 253 loop : -1.26 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 157 TYR 0.014 0.001 TYR B 187 PHE 0.012 0.001 PHE H 127 TRP 0.012 0.001 TRP B 457 HIS 0.003 0.001 HIS I 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15223) covalent geometry : angle 0.63600 / 0.31 (20509) hydrogen bonds : bond 0.03541 / 2.29 ( 750) hydrogen bonds : angle 4.59843 / 3.17 ( 2157) Misc. bond : bond 0.00013 / 0.01 ( 2) ********************** 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 132 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.404 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 198 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8487 (tpp) REVERT: H 199 GLU cc_start: 0.8334 (pm20) cc_final: 0.7901 (pp20) REVERT: J 48 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7735 (mt-10) REVERT: J 62 MET cc_start: 0.9120 (tpp) cc_final: 0.8803 (tpp) REVERT: J 193 ASN cc_start: 0.8948 (t0) cc_final: 0.8645 (t0) REVERT: G 55 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8320 (t) REVERT: G 64 LYS cc_start: 0.8478 (tttt) cc_final: 0.8225 (tttp) REVERT: F 135 MET cc_start: 0.8666 (tpt) cc_final: 0.8362 (mmm) REVERT: F 156 GLN cc_start: 0.9163 (mm110) cc_final: 0.8871 (mt0) REVERT: E 47 MET cc_start: 0.8928 (ppp) cc_final: 0.8694 (ppp) REVERT: E 52 MET cc_start: 0.9555 (mtm) cc_final: 0.9244 (mtp) REVERT: K 113 MET cc_start: 0.8390 (ppp) cc_final: 0.7905 (ppp) REVERT: K 136 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8557 (mm-30) REVERT: K 154 ASP cc_start: 0.8322 (t0) cc_final: 0.8057 (t0) REVERT: A 145 MET cc_start: 0.8436 (tpp) cc_final: 0.8043 (tpp) REVERT: A 192 ASN cc_start: 0.8569 (t0) cc_final: 0.8123 (t0) REVERT: B 249 MET cc_start: 0.5245 (ptm) cc_final: 0.4846 (tmm) REVERT: B 313 MET cc_start: 0.8059 (mmm) cc_final: 0.6714 (tpp) REVERT: B 351 MET cc_start: 0.8863 (tmm) cc_final: 0.8438 (tmm) REVERT: B 362 TRP cc_start: 0.9226 (m100) cc_final: 0.8835 (m100) REVERT: B 491 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8844 (mm-30) REVERT: B 521 MET cc_start: 0.9131 (mmp) cc_final: 0.8841 (mmt) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.1050 time to fit residues: 21.2762 Evaluate side-chains 129 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 268 ILE Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain F residue 68 ILE Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 491 GLU Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 549 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 87 optimal weight: 0.5980 chunk 102 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 172 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 220 GLN ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 HIS B 559 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.042632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033556 restraints weight = 96418.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.034806 restraints weight = 48446.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.035635 restraints weight = 30612.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036237 restraints weight = 22076.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036647 restraints weight = 17374.149| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15225 Z= 0.119 Angle : 0.632 11.350 20509 Z= 0.313 Chirality : 0.042 0.285 2321 Planarity : 0.003 0.050 2556 Dihedral : 5.002 54.398 1981 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.19 % Allowed : 17.81 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1756 helix: 1.42 (0.18), residues: 875 sheet: -0.33 (0.32), residues: 251 loop : -1.23 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 157 TYR 0.014 0.001 TYR B 187 PHE 0.011 0.001 PHE I 49 TRP 0.012 0.001 TRP B 457 HIS 0.003 0.000 HIS J 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (15223) covalent geometry : angle 0.63202 / 0.31 (20509) hydrogen bonds : bond 0.03534 / 2.27 ( 750) hydrogen bonds : angle 4.57559 / 3.16 ( 2157) Misc. bond : bond 0.00010 / 0.00 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.61 seconds wall clock time: 49 minutes 5.11 seconds (2945.11 seconds total)