Starting phenix.real_space_refine on Wed Mar 4 17:09:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kmt_22928/03_2026/7kmt_22928.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kmt_22928/03_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_22928/03_2026/7kmt_22928.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kmt_22928/03_2026/7kmt_22928.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kmt_22928/03_2026/7kmt_22928.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kmt_22928/03_2026/7kmt_22928.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 3.14, per 1000 atoms: 0.21 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: 1.40 Conformation dependent library (CDL) restraints added in 495.4 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: 0.35 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: 2.19 Time building geometry restraints manager: 1.74 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: 1.440 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 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 covalent geometry : bond 0.00447 (15223) covalent geometry : angle 0.78985 (20509) hydrogen bonds : bond 0.13705 ( 750) hydrogen bonds : angle 6.89019 ( 2157) Misc. bond : bond 0.02963 ( 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 : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 136 THR cc_start: 0.9246 (p) cc_final: 0.9015 (t) REVERT: J 48 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7837 (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: 0.8577 (mt0) REVERT: E 47 MET cc_start: 0.8869 (ppp) cc_final: 0.8595 (ppp) REVERT: E 57 MET cc_start: 0.8656 (tpt) cc_final: 0.8110 (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: 0.7769 (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: 0.8335 (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: 0.8948 (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: 0.1293 time to fit residues: 38.4037 Evaluate side-chains 121 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: J 257 GLN G 33 ASN G 56 GLN I 181 ASN F 55 HIS A 93 GLN B 76 GLN B 156 HIS B 209 HIS B 310 GLN B 477 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.042292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.032991 restraints weight = 99239.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034202 restraints weight = 49942.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035030 restraints weight = 31972.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.035609 restraints weight = 23403.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.036003 restraints weight = 18699.433| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 15225 Z= 0.222 Angle : 0.697 14.555 20509 Z= 0.362 Chirality : 0.044 0.167 2321 Planarity : 0.004 0.049 2556 Dihedral : 6.200 59.860 1981 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.60 % Allowed : 9.23 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.65 (0.20), residues: 1756 helix: 0.70 (0.18), residues: 870 sheet: -1.39 (0.30), residues: 264 loop : -1.53 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 157 TYR 0.021 0.002 TYR F 57 PHE 0.025 0.002 PHE B 270 TRP 0.016 0.002 TRP F 162 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00501 (15223) covalent geometry : angle 0.69669 (20509) hydrogen bonds : bond 0.04687 ( 750) hydrogen bonds : angle 5.40866 ( 2157) Misc. bond : bond 0.00081 ( 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 146 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 136 THR cc_start: 0.9397 (p) cc_final: 0.9157 (t) REVERT: H 214 MET cc_start: 0.9370 (tpp) cc_final: 0.9141 (mmm) REVERT: J 48 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7808 (mt-10) REVERT: G 64 LYS cc_start: 0.8644 (tttt) cc_final: 0.8311 (tttp) REVERT: F 156 GLN cc_start: 0.9247 (mm110) cc_final: 0.8771 (mt0) REVERT: E 47 MET cc_start: 0.9092 (ppp) cc_final: 0.8704 (ppp) REVERT: E 52 MET cc_start: 0.9555 (mtm) cc_final: 0.9003 (mtp) REVERT: E 57 MET cc_start: 0.8818 (tpt) cc_final: 0.8020 (tpp) REVERT: K 49 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8890 (mt-10) REVERT: K 50 ASP cc_start: 0.8633 (t0) cc_final: 0.8295 (t0) REVERT: K 113 MET cc_start: 0.8439 (ppp) cc_final: 0.8080 (ppp) REVERT: K 136 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8601 (mm-30) REVERT: K 140 LEU cc_start: 0.9423 (mp) cc_final: 0.9197 (mm) REVERT: K 154 ASP cc_start: 0.7868 (t0) cc_final: 0.7531 (t0) REVERT: K 171 LYS cc_start: 0.9421 (mttm) cc_final: 0.9032 (mttm) REVERT: A 145 MET cc_start: 0.8894 (tpp) cc_final: 0.8673 (tpp) REVERT: A 192 ASN cc_start: 0.8527 (t0) cc_final: 0.8059 (t0) REVERT: B 261 CYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8744 (t) REVERT: B 343 LEU cc_start: 0.9485 (mt) cc_final: 0.9195 (mt) REVERT: B 351 MET cc_start: 0.8560 (tmm) cc_final: 0.8247 (tmm) REVERT: B 464 MET cc_start: 0.9071 (mmm) cc_final: 0.8754 (tpp) REVERT: B 484 GLU cc_start: 0.8859 (tp30) cc_final: 0.8442 (tp30) REVERT: B 523 LEU cc_start: 0.9487 (tp) cc_final: 0.9149 (tt) outliers start: 10 outliers final: 5 residues processed: 142 average time/residue: 0.1114 time to fit residues: 24.5379 Evaluate side-chains 118 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain B residue 22 VAL 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: 0.9980 chunk 116 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 138 optimal weight: 0.0040 chunk 75 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3191 r_free = 0.3191 target = 0.042917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.033775 restraints weight = 96529.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035036 restraints weight = 48415.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.035888 restraints weight = 30348.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.036481 restraints weight = 21902.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.036883 restraints weight = 17287.169| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15225 Z= 0.134 Angle : 0.596 12.707 20509 Z= 0.307 Chirality : 0.042 0.177 2321 Planarity : 0.004 0.042 2556 Dihedral : 5.782 57.144 1981 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.31 % Allowed : 11.85 % Favored : 86.84 % 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: -0.28 (0.20), residues: 1756 helix: 0.98 (0.18), residues: 875 sheet: -1.15 (0.30), residues: 264 loop : -1.34 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 192 TYR 0.017 0.001 TYR B 187 PHE 0.015 0.001 PHE E 242 TRP 0.012 0.001 TRP F 162 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00311 (15223) covalent geometry : angle 0.59586 (20509) hydrogen bonds : bond 0.04077 ( 750) hydrogen bonds : angle 4.96150 ( 2157) Misc. bond : bond 0.00031 ( 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 150 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 44 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8689 (t80) REVERT: H 200 MET cc_start: 0.9089 (mpp) cc_final: 0.8609 (mmm) REVERT: H 214 MET cc_start: 0.9363 (tpp) cc_final: 0.9105 (mmm) REVERT: H 220 GLN cc_start: 0.7749 (tt0) cc_final: 0.7245 (tt0) REVERT: J 48 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7776 (mt-10) REVERT: G 64 LYS cc_start: 0.8641 (tttt) cc_final: 0.8347 (tttp) REVERT: F 88 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8861 (pt0) REVERT: F 156 GLN cc_start: 0.9230 (mm110) cc_final: 0.8865 (mt0) REVERT: E 47 MET cc_start: 0.9056 (ppp) cc_final: 0.8628 (ppp) REVERT: E 52 MET cc_start: 0.9507 (mtm) cc_final: 0.9098 (mtp) REVERT: K 50 ASP cc_start: 0.8628 (t0) cc_final: 0.8342 (t0) REVERT: K 113 MET cc_start: 0.8336 (ppp) cc_final: 0.8048 (ppp) REVERT: K 136 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8561 (mm-30) REVERT: K 140 LEU cc_start: 0.9384 (mp) cc_final: 0.9168 (mm) REVERT: K 150 TYR cc_start: 0.8545 (t80) cc_final: 0.8328 (t80) REVERT: K 154 ASP cc_start: 0.7876 (t0) cc_final: 0.7468 (t0) REVERT: K 171 LYS cc_start: 0.9425 (mttm) cc_final: 0.9008 (mttm) REVERT: A 192 ASN cc_start: 0.8553 (t0) cc_final: 0.8088 (t0) REVERT: B 343 LEU cc_start: 0.9488 (mt) cc_final: 0.9212 (mt) REVERT: B 351 MET cc_start: 0.8525 (tmm) cc_final: 0.8119 (tmm) REVERT: B 484 GLU cc_start: 0.8814 (tp30) cc_final: 0.8332 (tp30) REVERT: B 491 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8805 (mm-30) REVERT: B 521 MET cc_start: 0.9318 (mmp) cc_final: 0.8890 (mmp) outliers start: 22 outliers final: 7 residues processed: 144 average time/residue: 0.1040 time to fit residues: 24.0318 Evaluate side-chains 124 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 44 PHE Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain F residue 88 GLU 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 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: 3.9990 chunk 129 optimal weight: 0.0050 chunk 100 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 HIS K 52 GLN K 129 ASN B 559 GLN B 641 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.042130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032938 restraints weight = 98720.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.034148 restraints weight = 50345.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.034971 restraints weight = 32330.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.035532 restraints weight = 23683.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.035907 restraints weight = 18981.395| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 15225 Z= 0.183 Angle : 0.605 12.673 20509 Z= 0.315 Chirality : 0.042 0.172 2321 Planarity : 0.004 0.039 2556 Dihedral : 5.643 58.672 1981 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.20 % Allowed : 12.51 % Favored : 85.29 % 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: -0.22 (0.21), residues: 1756 helix: 1.03 (0.18), residues: 873 sheet: -1.03 (0.30), residues: 266 loop : -1.37 (0.26), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 192 TYR 0.015 0.001 TYR B 187 PHE 0.019 0.001 PHE I 127 TRP 0.011 0.001 TRP F 162 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00418 (15223) covalent geometry : angle 0.60532 (20509) hydrogen bonds : bond 0.04053 ( 750) hydrogen bonds : angle 4.94734 ( 2157) Misc. bond : bond 0.00045 ( 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 158 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.621 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: 0.8849 (OUTLIER) cc_final: 0.8584 (t80) REVERT: H 200 MET cc_start: 0.9135 (mpp) cc_final: 0.8723 (mmm) REVERT: H 214 MET cc_start: 0.9340 (tpp) cc_final: 0.9075 (mmm) REVERT: H 220 GLN cc_start: 0.7881 (tt0) cc_final: 0.7319 (tt0) REVERT: J 48 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7791 (mt-10) REVERT: G 36 GLN cc_start: 0.9503 (mp10) cc_final: 0.9217 (mp10) REVERT: G 64 LYS cc_start: 0.8566 (tttt) cc_final: 0.8272 (tttp) REVERT: F 88 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8870 (pt0) REVERT: F 156 GLN cc_start: 0.9241 (mm110) cc_final: 0.8895 (mt0) REVERT: E 47 MET cc_start: 0.9011 (ppp) cc_final: 0.8585 (ppp) REVERT: E 52 MET cc_start: 0.9508 (mtm) cc_final: 0.9202 (mtp) REVERT: K 50 ASP cc_start: 0.8584 (t0) cc_final: 0.8258 (t0) REVERT: K 113 MET cc_start: 0.8377 (ppp) cc_final: 0.8134 (ppp) REVERT: K 140 LEU cc_start: 0.9417 (mp) cc_final: 0.9208 (mm) REVERT: K 154 ASP cc_start: 0.7934 (t0) cc_final: 0.7708 (t0) REVERT: K 171 LYS cc_start: 0.9398 (mttm) cc_final: 0.9142 (mttm) REVERT: A 145 MET cc_start: 0.8835 (tpp) cc_final: 0.8563 (tpp) REVERT: A 192 ASN cc_start: 0.8576 (t0) cc_final: 0.8101 (t0) REVERT: B 249 MET cc_start: 0.5632 (OUTLIER) cc_final: 0.5291 (tmm) REVERT: B 343 LEU cc_start: 0.9482 (mt) cc_final: 0.9229 (mt) REVERT: B 351 MET cc_start: 0.8683 (tmm) cc_final: 0.8239 (tmm) REVERT: B 484 GLU cc_start: 0.8880 (tp30) cc_final: 0.8404 (tp30) REVERT: B 521 MET cc_start: 0.9276 (mmp) cc_final: 0.8866 (mmp) outliers start: 37 outliers final: 16 residues processed: 149 average time/residue: 0.1053 time to fit residues: 24.7021 Evaluate side-chains 132 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 G residue 55 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain F residue 88 GLU 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 249 MET Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 471 THR 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: 6.9990 chunk 1 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 79 optimal weight: 0.0060 chunk 176 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.042718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.033514 restraints weight = 97530.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.034752 restraints weight = 49786.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.035588 restraints weight = 31729.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.036166 restraints weight = 23171.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.036568 restraints weight = 18477.921| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15225 Z= 0.128 Angle : 0.583 12.143 20509 Z= 0.298 Chirality : 0.041 0.178 2321 Planarity : 0.003 0.040 2556 Dihedral : 5.482 57.024 1981 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.43 % Allowed : 14.53 % Favored : 84.04 % 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: 0.02 (0.21), residues: 1756 helix: 1.17 (0.18), residues: 876 sheet: -0.90 (0.31), residues: 261 loop : -1.20 (0.26), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 157 TYR 0.016 0.001 TYR B 187 PHE 0.012 0.001 PHE I 127 TRP 0.010 0.001 TRP B 457 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00299 (15223) covalent geometry : angle 0.58346 (20509) hydrogen bonds : bond 0.03796 ( 750) hydrogen bonds : angle 4.76652 ( 2157) Misc. bond : bond 0.00024 ( 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 150 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 191 MET cc_start: 0.7813 (mmm) cc_final: 0.7445 (mmm) REVERT: H 200 MET cc_start: 0.9036 (mpp) cc_final: 0.8569 (mmm) REVERT: H 214 MET cc_start: 0.9278 (tpp) cc_final: 0.9060 (tpt) REVERT: H 220 GLN cc_start: 0.7547 (tt0) cc_final: 0.7162 (tt0) REVERT: J 48 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7771 (mt-10) REVERT: J 193 ASN cc_start: 0.8901 (t0) cc_final: 0.8648 (t0) REVERT: G 36 GLN cc_start: 0.9501 (mp10) cc_final: 0.9078 (mp10) REVERT: G 39 GLU cc_start: 0.8492 (mp0) cc_final: 0.7312 (mp0) REVERT: G 64 LYS cc_start: 0.8600 (tttt) cc_final: 0.8295 (tttp) REVERT: F 88 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8870 (pt0) REVERT: F 156 GLN cc_start: 0.9205 (mm110) cc_final: 0.8891 (mt0) REVERT: E 47 MET cc_start: 0.8979 (ppp) cc_final: 0.8471 (ppp) REVERT: E 52 MET cc_start: 0.9524 (mtm) cc_final: 0.9156 (mtp) REVERT: K 50 ASP cc_start: 0.8712 (t0) cc_final: 0.8360 (t0) REVERT: K 113 MET cc_start: 0.8241 (ppp) cc_final: 0.7779 (ppp) REVERT: K 136 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8517 (mm-30) REVERT: K 154 ASP cc_start: 0.7988 (t0) cc_final: 0.7688 (t0) REVERT: K 171 LYS cc_start: 0.9406 (mttm) cc_final: 0.9118 (mttm) REVERT: A 145 MET cc_start: 0.9035 (tpp) cc_final: 0.8830 (tpp) REVERT: A 192 ASN cc_start: 0.8555 (t0) cc_final: 0.8043 (t0) REVERT: B 343 LEU cc_start: 0.9510 (mt) cc_final: 0.9285 (mt) REVERT: B 351 MET cc_start: 0.8751 (tmm) cc_final: 0.8281 (tmm) REVERT: B 484 GLU cc_start: 0.8911 (tp30) cc_final: 0.8421 (tp30) REVERT: B 521 MET cc_start: 0.9274 (mmp) cc_final: 0.8883 (mmp) outliers start: 24 outliers final: 15 residues processed: 144 average time/residue: 0.1034 time to fit residues: 23.6117 Evaluate side-chains 127 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain J residue 200 VAL 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 88 GLU 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 255 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 471 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 83 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 94 optimal weight: 0.0870 chunk 47 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 155 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3165 r_free = 0.3165 target = 0.042114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.032969 restraints weight = 98372.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.034171 restraints weight = 50260.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.034986 restraints weight = 32314.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.035548 restraints weight = 23661.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.035947 restraints weight = 18930.773| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15225 Z= 0.164 Angle : 0.596 12.134 20509 Z= 0.308 Chirality : 0.041 0.169 2321 Planarity : 0.004 0.049 2556 Dihedral : 5.465 56.321 1981 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.61 % Allowed : 15.31 % Favored : 83.09 % 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: -0.03 (0.20), residues: 1756 helix: 1.14 (0.18), residues: 875 sheet: -0.85 (0.31), residues: 256 loop : -1.27 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 485 TYR 0.014 0.001 TYR B 187 PHE 0.017 0.001 PHE I 127 TRP 0.011 0.001 TRP B 457 HIS 0.004 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00378 (15223) covalent geometry : angle 0.59627 (20509) hydrogen bonds : bond 0.03818 ( 750) hydrogen bonds : angle 4.80296 ( 2157) Misc. bond : bond 0.00029 ( 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 147 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 200 MET cc_start: 0.9058 (mpp) cc_final: 0.8565 (mmm) REVERT: H 214 MET cc_start: 0.9352 (tpp) cc_final: 0.9113 (mmm) REVERT: H 220 GLN cc_start: 0.7647 (tt0) cc_final: 0.7317 (tt0) REVERT: J 48 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7811 (mt-10) REVERT: J 193 ASN cc_start: 0.8892 (t0) cc_final: 0.8625 (t0) REVERT: G 64 LYS cc_start: 0.8558 (tttt) cc_final: 0.8203 (tttp) REVERT: F 156 GLN cc_start: 0.9237 (mm110) cc_final: 0.8902 (mt0) REVERT: E 47 MET cc_start: 0.8984 (ppp) cc_final: 0.8470 (ppp) REVERT: E 52 MET cc_start: 0.9510 (mtm) cc_final: 0.9157 (mtp) REVERT: K 50 ASP cc_start: 0.8630 (t0) cc_final: 0.8272 (t0) REVERT: K 113 MET cc_start: 0.8299 (ppp) cc_final: 0.7846 (ppp) REVERT: K 136 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8736 (mm-30) REVERT: K 154 ASP cc_start: 0.8090 (t0) cc_final: 0.7807 (t0) REVERT: K 171 LYS cc_start: 0.9373 (mttm) cc_final: 0.9140 (mttm) REVERT: A 192 ASN cc_start: 0.8586 (t0) cc_final: 0.8120 (t0) REVERT: B 249 MET cc_start: 0.5636 (ptm) cc_final: 0.5172 (tmm) REVERT: B 343 LEU cc_start: 0.9481 (mt) cc_final: 0.9266 (mt) REVERT: B 351 MET cc_start: 0.8697 (tmm) cc_final: 0.8248 (tmm) REVERT: B 484 GLU cc_start: 0.8838 (tp30) cc_final: 0.8317 (tp30) REVERT: B 521 MET cc_start: 0.9238 (mmp) cc_final: 0.8806 (mmp) outliers start: 27 outliers final: 17 residues processed: 142 average time/residue: 0.0943 time to fit residues: 21.7362 Evaluate side-chains 127 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 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 E residue 93 HIS Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 471 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 100 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 153 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 174 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3172 r_free = 0.3172 target = 0.042301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.033157 restraints weight = 98324.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034374 restraints weight = 50094.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.035205 restraints weight = 32096.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.035766 restraints weight = 23395.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036169 restraints weight = 18718.171| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 15225 Z= 0.144 Angle : 0.602 11.706 20509 Z= 0.308 Chirality : 0.042 0.276 2321 Planarity : 0.004 0.049 2556 Dihedral : 5.454 56.621 1981 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.61 % Allowed : 15.90 % Favored : 82.49 % 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: 0.02 (0.21), residues: 1756 helix: 1.18 (0.18), residues: 879 sheet: -0.75 (0.31), residues: 253 loop : -1.31 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 157 TYR 0.015 0.001 TYR B 187 PHE 0.015 0.001 PHE I 127 TRP 0.011 0.001 TRP B 457 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00336 (15223) covalent geometry : angle 0.60222 (20509) hydrogen bonds : bond 0.03749 ( 750) hydrogen bonds : angle 4.76277 ( 2157) Misc. bond : bond 0.00023 ( 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 145 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 200 MET cc_start: 0.9036 (mpp) cc_final: 0.8674 (mmm) REVERT: H 214 MET cc_start: 0.9367 (tpp) cc_final: 0.9089 (mmm) REVERT: H 220 GLN cc_start: 0.7696 (tt0) cc_final: 0.7340 (mt0) REVERT: J 48 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7808 (mt-10) REVERT: J 193 ASN cc_start: 0.8924 (t0) cc_final: 0.8638 (t0) REVERT: G 64 LYS cc_start: 0.8537 (tttt) cc_final: 0.8246 (tttp) REVERT: I 13 MET cc_start: 0.8898 (ppp) cc_final: 0.8590 (ppp) REVERT: F 156 GLN cc_start: 0.9249 (mm110) cc_final: 0.8924 (mt0) REVERT: E 47 MET cc_start: 0.8979 (ppp) cc_final: 0.8450 (ppp) REVERT: E 52 MET cc_start: 0.9510 (mtm) cc_final: 0.9170 (mtp) REVERT: K 50 ASP cc_start: 0.8705 (t0) cc_final: 0.8320 (t0) REVERT: K 113 MET cc_start: 0.8255 (ppp) cc_final: 0.7827 (ppp) REVERT: K 154 ASP cc_start: 0.8024 (t0) cc_final: 0.7755 (t0) REVERT: K 171 LYS cc_start: 0.9378 (mttm) cc_final: 0.9154 (mttm) REVERT: A 71 ARG cc_start: 0.8865 (pmt-80) cc_final: 0.8595 (pmt-80) REVERT: A 192 ASN cc_start: 0.8571 (t0) cc_final: 0.8110 (t0) REVERT: B 249 MET cc_start: 0.5712 (ptm) cc_final: 0.5082 (tmm) REVERT: B 313 MET cc_start: 0.7791 (mmm) cc_final: 0.6403 (tpp) REVERT: B 351 MET cc_start: 0.8700 (tmm) cc_final: 0.8258 (tmm) REVERT: B 362 TRP cc_start: 0.9174 (m100) cc_final: 0.8823 (m100) REVERT: B 484 GLU cc_start: 0.8871 (tp30) cc_final: 0.8340 (tp30) REVERT: B 521 MET cc_start: 0.9172 (mmp) cc_final: 0.8825 (mmp) outliers start: 27 outliers final: 19 residues processed: 140 average time/residue: 0.1036 time to fit residues: 23.2593 Evaluate side-chains 133 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.642 ------------------------------------------------------------------------------- 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 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 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 63 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 471 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 5 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 172 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3174 r_free = 0.3174 target = 0.042390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033266 restraints weight = 98119.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.034483 restraints weight = 50120.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.035319 restraints weight = 32083.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.035894 restraints weight = 23354.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036299 restraints weight = 18566.793| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15225 Z= 0.138 Angle : 0.617 11.256 20509 Z= 0.311 Chirality : 0.041 0.244 2321 Planarity : 0.003 0.049 2556 Dihedral : 5.418 58.904 1981 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.37 % Allowed : 16.44 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.21), residues: 1756 helix: 1.29 (0.18), residues: 873 sheet: -0.65 (0.32), residues: 244 loop : -1.32 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 157 TYR 0.014 0.001 TYR B 187 PHE 0.014 0.001 PHE I 127 TRP 0.011 0.001 TRP B 457 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00323 (15223) covalent geometry : angle 0.61697 (20509) hydrogen bonds : bond 0.03713 ( 750) hydrogen bonds : angle 4.70936 ( 2157) Misc. bond : bond 0.00019 ( 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 147 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.601 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 48 SER cc_start: 0.8738 (m) cc_final: 0.8498 (p) REVERT: H 200 MET cc_start: 0.9048 (mpp) cc_final: 0.8692 (mmm) REVERT: H 214 MET cc_start: 0.9329 (tpp) cc_final: 0.9012 (tpt) REVERT: H 220 GLN cc_start: 0.7691 (tt0) cc_final: 0.7348 (mt0) REVERT: J 48 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7799 (mt-10) REVERT: J 193 ASN cc_start: 0.8916 (t0) cc_final: 0.8632 (t0) REVERT: J 255 MET cc_start: 0.8703 (ppp) cc_final: 0.8355 (ppp) REVERT: G 64 LYS cc_start: 0.8519 (tttt) cc_final: 0.8219 (tttp) REVERT: G 66 ASP cc_start: 0.7397 (t0) cc_final: 0.7177 (t0) REVERT: F 156 GLN cc_start: 0.9242 (mm110) cc_final: 0.8904 (mt0) REVERT: E 47 MET cc_start: 0.8982 (ppp) cc_final: 0.8439 (ppp) REVERT: E 52 MET cc_start: 0.9507 (mtm) cc_final: 0.9165 (mtp) REVERT: K 50 ASP cc_start: 0.8716 (t0) cc_final: 0.8337 (t0) REVERT: K 113 MET cc_start: 0.8250 (ppp) cc_final: 0.7844 (ppp) REVERT: K 136 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8444 (mm-30) REVERT: K 154 ASP cc_start: 0.8146 (t0) cc_final: 0.7883 (t0) REVERT: A 71 ARG cc_start: 0.8923 (pmt-80) cc_final: 0.8635 (pmt-80) REVERT: A 192 ASN cc_start: 0.8564 (t0) cc_final: 0.8114 (t0) REVERT: B 249 MET cc_start: 0.5392 (ptm) cc_final: 0.5003 (tmm) REVERT: B 351 MET cc_start: 0.8684 (tmm) cc_final: 0.8267 (tmm) REVERT: B 362 TRP cc_start: 0.9199 (m100) cc_final: 0.8826 (m100) REVERT: B 484 GLU cc_start: 0.8904 (tp30) cc_final: 0.8423 (tp30) REVERT: B 521 MET cc_start: 0.9138 (mmp) cc_final: 0.8810 (mmt) outliers start: 23 outliers final: 19 residues processed: 142 average time/residue: 0.1080 time to fit residues: 24.0803 Evaluate side-chains 133 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 164 VAL 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 63 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 518 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 138 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 46 optimal weight: 0.0570 chunk 104 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3190 r_free = 0.3190 target = 0.042763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033765 restraints weight = 96171.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.034994 restraints weight = 48297.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.035840 restraints weight = 30576.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.036423 restraints weight = 22070.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.036741 restraints weight = 17397.143| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3399 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= 0.119 Angle : 0.627 11.967 20509 Z= 0.312 Chirality : 0.042 0.274 2321 Planarity : 0.003 0.054 2556 Dihedral : 5.338 57.989 1981 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.31 % Allowed : 16.62 % Favored : 82.07 % 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: 0.17 (0.21), residues: 1756 helix: 1.31 (0.18), residues: 872 sheet: -0.52 (0.32), residues: 242 loop : -1.28 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 157 TYR 0.015 0.001 TYR B 187 PHE 0.011 0.001 PHE H 127 TRP 0.011 0.001 TRP B 457 HIS 0.003 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00277 (15223) covalent geometry : angle 0.62652 (20509) hydrogen bonds : bond 0.03649 ( 750) hydrogen bonds : angle 4.66716 ( 2157) Misc. bond : bond 0.00015 ( 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 145 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.530 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 48 SER cc_start: 0.8686 (m) cc_final: 0.8435 (p) REVERT: H 199 GLU cc_start: 0.8429 (pm20) cc_final: 0.8108 (pp20) REVERT: H 200 MET cc_start: 0.9003 (mpp) cc_final: 0.8420 (mmm) REVERT: H 214 MET cc_start: 0.9331 (tpp) cc_final: 0.8937 (tpt) REVERT: H 220 GLN cc_start: 0.7643 (tt0) cc_final: 0.7303 (tt0) REVERT: J 48 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7793 (mt-10) REVERT: J 193 ASN cc_start: 0.8874 (t0) cc_final: 0.8572 (t0) REVERT: J 255 MET cc_start: 0.8708 (ppp) cc_final: 0.8440 (ppp) REVERT: G 64 LYS cc_start: 0.8478 (tttt) cc_final: 0.8193 (tttp) REVERT: F 156 GLN cc_start: 0.9224 (mm110) cc_final: 0.8859 (mt0) REVERT: E 47 MET cc_start: 0.8906 (ppp) cc_final: 0.8651 (ppp) REVERT: E 52 MET cc_start: 0.9485 (mtm) cc_final: 0.9185 (mtp) REVERT: K 50 ASP cc_start: 0.8714 (t0) cc_final: 0.8344 (t0) REVERT: K 113 MET cc_start: 0.8224 (ppp) cc_final: 0.7836 (ppp) REVERT: K 136 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8476 (mm-30) REVERT: K 154 ASP cc_start: 0.8204 (t0) cc_final: 0.7940 (t0) REVERT: A 71 ARG cc_start: 0.8921 (pmt-80) cc_final: 0.8664 (pmt-80) REVERT: A 192 ASN cc_start: 0.8552 (t0) cc_final: 0.8087 (t0) REVERT: B 249 MET cc_start: 0.5559 (ptm) cc_final: 0.4944 (tmm) REVERT: B 313 MET cc_start: 0.7821 (mmm) cc_final: 0.6423 (tpp) REVERT: B 351 MET cc_start: 0.8690 (tmm) cc_final: 0.8288 (tmm) REVERT: B 362 TRP cc_start: 0.9176 (m100) cc_final: 0.8742 (m100) REVERT: B 484 GLU cc_start: 0.8948 (tp30) cc_final: 0.8414 (tp30) REVERT: B 521 MET cc_start: 0.9146 (mmp) cc_final: 0.8784 (mmt) outliers start: 22 outliers final: 17 residues processed: 141 average time/residue: 0.1118 time to fit residues: 24.4432 Evaluate side-chains 130 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 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 164 VAL 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 63 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 665 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 61 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 147 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 184 HIS ** J 243 ASN ** 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 = 0.3188 r_free = 0.3188 target = 0.042772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033539 restraints weight = 98079.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.034781 restraints weight = 49755.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.035623 restraints weight = 31778.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.036209 restraints weight = 23122.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.036607 restraints weight = 18350.677| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15225 Z= 0.129 Angle : 0.651 14.684 20509 Z= 0.321 Chirality : 0.042 0.329 2321 Planarity : 0.004 0.052 2556 Dihedral : 5.267 59.038 1981 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.19 % Allowed : 16.50 % Favored : 82.31 % 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: 0.19 (0.21), residues: 1756 helix: 1.32 (0.18), residues: 871 sheet: -0.44 (0.32), residues: 242 loop : -1.28 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 157 TYR 0.014 0.001 TYR B 187 PHE 0.012 0.001 PHE I 127 TRP 0.013 0.001 TRP B 457 HIS 0.003 0.001 HIS F 55 Details of bonding type rmsd covalent geometry : bond 0.00300 (15223) covalent geometry : angle 0.65081 (20509) hydrogen bonds : bond 0.03706 ( 750) hydrogen bonds : angle 4.67752 ( 2157) Misc. bond : bond 0.00014 ( 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 137 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.587 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 48 SER cc_start: 0.8654 (m) cc_final: 0.8394 (p) REVERT: H 191 MET cc_start: 0.7810 (mmm) cc_final: 0.7198 (mmm) REVERT: H 199 GLU cc_start: 0.8404 (pm20) cc_final: 0.7974 (pp20) REVERT: H 200 MET cc_start: 0.8980 (mpp) cc_final: 0.7917 (mpp) REVERT: H 214 MET cc_start: 0.9348 (tpp) cc_final: 0.8945 (tpt) REVERT: H 220 GLN cc_start: 0.7666 (tt0) cc_final: 0.7376 (mt0) REVERT: J 48 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7768 (mt-10) REVERT: J 193 ASN cc_start: 0.8880 (t0) cc_final: 0.8578 (t0) REVERT: J 255 MET cc_start: 0.8683 (ppp) cc_final: 0.8465 (ppp) REVERT: G 64 LYS cc_start: 0.8453 (tttt) cc_final: 0.8174 (tttp) REVERT: F 156 GLN cc_start: 0.9217 (mm110) cc_final: 0.8869 (mt0) REVERT: E 47 MET cc_start: 0.8922 (ppp) cc_final: 0.8671 (ppp) REVERT: E 52 MET cc_start: 0.9515 (mtm) cc_final: 0.9198 (mtp) REVERT: K 50 ASP cc_start: 0.8739 (t0) cc_final: 0.8358 (t0) REVERT: K 113 MET cc_start: 0.8349 (ppp) cc_final: 0.7877 (ppp) REVERT: K 136 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8476 (mm-30) REVERT: K 154 ASP cc_start: 0.8238 (t0) cc_final: 0.7977 (t0) REVERT: A 71 ARG cc_start: 0.8916 (pmt-80) cc_final: 0.8699 (pmt-80) REVERT: A 192 ASN cc_start: 0.8561 (t0) cc_final: 0.8087 (t0) REVERT: B 249 MET cc_start: 0.5571 (ptm) cc_final: 0.4994 (tmm) REVERT: B 313 MET cc_start: 0.7950 (mmm) cc_final: 0.6600 (tpp) REVERT: B 351 MET cc_start: 0.8745 (tmm) cc_final: 0.8351 (tmm) REVERT: B 362 TRP cc_start: 0.9182 (m100) cc_final: 0.8757 (m100) REVERT: B 484 GLU cc_start: 0.8973 (tp30) cc_final: 0.8427 (tp30) REVERT: B 521 MET cc_start: 0.9147 (mmp) cc_final: 0.8779 (mmt) outliers start: 20 outliers final: 19 residues processed: 132 average time/residue: 0.1076 time to fit residues: 22.1359 Evaluate side-chains 131 residues out of total 1680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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 164 VAL 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 63 LEU Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 471 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 87 optimal weight: 0.6980 chunk 102 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 170 optimal weight: 0.9990 chunk 172 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3177 r_free = 0.3177 target = 0.042426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.033300 restraints weight = 97914.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.034506 restraints weight = 50528.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.035334 restraints weight = 32528.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.035880 restraints weight = 23749.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036300 restraints weight = 18977.238| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 15225 Z= 0.149 Angle : 0.657 12.057 20509 Z= 0.325 Chirality : 0.042 0.370 2321 Planarity : 0.004 0.051 2556 Dihedral : 5.246 58.026 1981 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.13 % Allowed : 16.74 % Favored : 82.13 % 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: 0.17 (0.21), residues: 1756 helix: 1.30 (0.18), residues: 871 sheet: -0.47 (0.32), residues: 244 loop : -1.28 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 485 TYR 0.013 0.001 TYR B 187 PHE 0.015 0.001 PHE I 127 TRP 0.013 0.001 TRP B 457 HIS 0.006 0.001 HIS F 55 Details of bonding type rmsd covalent geometry : bond 0.00348 (15223) covalent geometry : angle 0.65693 (20509) hydrogen bonds : bond 0.03766 ( 750) hydrogen bonds : angle 4.70978 ( 2157) Misc. bond : bond 0.00016 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2560.42 seconds wall clock time: 45 minutes 4.60 seconds (2704.60 seconds total)