Starting phenix.real_space_refine on Wed Mar 4 17:23:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cx2_27034/03_2026/8cx2_27034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cx2_27034/03_2026/8cx2_27034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8cx2_27034/03_2026/8cx2_27034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cx2_27034/03_2026/8cx2_27034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8cx2_27034/03_2026/8cx2_27034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cx2_27034/03_2026/8cx2_27034.map" } resolution = 3.2 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= 0.001 sd= 0.039 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 18 5.49 5 S 92 5.16 5 C 9525 2.51 5 N 2668 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 15041 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3211 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain: "B" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1468 Classifications: {'peptide': 176} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 166} Chain: "C" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1254 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "D" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "F" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3211 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1468 Classifications: {'peptide': 176} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 166} Chain: "H" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1275 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "I" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "K" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 4} Link IDs: {'rna2p': 4, 'rna3p': 4} Chain: "L" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2457 SG CYS A 288 34.823 21.522 36.834 1.00104.36 S ATOM 2480 SG CYS A 291 35.490 24.180 37.316 1.00 93.76 S ATOM 824 SG CYS A 97 55.944 55.618 50.636 1.00 46.37 S ATOM 846 SG CYS A 100 58.143 55.092 52.191 1.00 56.54 S ATOM 4195 SG CYS B 114 32.332 86.770 53.473 1.00 94.58 S ATOM 4339 SG CYS B 133 35.703 85.325 54.750 1.00 90.36 S ATOM 9776 SG CYS F 288 18.165 56.352 107.513 1.00132.85 S ATOM 9799 SG CYS F 291 21.029 56.636 106.539 1.00124.22 S ATOM 8143 SG CYS F 97 51.398 67.782 84.004 1.00 49.52 S ATOM 8165 SG CYS F 100 50.987 70.212 82.350 1.00 58.78 S ATOM 11514 SG CYS G 114 76.648 38.602 81.181 1.00162.59 S ATOM 11658 SG CYS G 133 75.213 41.532 79.251 1.00156.40 S Time building chain proxies: 3.54, per 1000 atoms: 0.24 Number of scatterers: 15041 At special positions: 0 Unit cell: (136.105, 140.28, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 92 16.00 P 18 15.00 O 2732 8.00 N 2668 7.00 C 9525 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=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 528.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 257 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 288 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 291 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 65 " pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 139 " pdb="ZN ZN B 201 " - pdb=" NE2 HIS B 108 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 114 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 133 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 291 " pdb="ZN ZN F 501 " - pdb=" ND1 HIS F 257 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 288 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 65 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 100 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 97 " pdb=" ZN G 201 " pdb="ZN ZN G 201 " - pdb=" NE2 HIS G 139 " pdb="ZN ZN G 201 " - pdb=" NE2 HIS G 108 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 114 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " Number of angles added : 4 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 40.1% alpha, 21.1% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.664A pdb=" N LYS A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 177 through 194 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 257 through 266 Processing helix chain 'A' and resid 267 through 270 removed outlier: 3.598A pdb=" N LYS A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 267 through 270' Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 319 through 332 removed outlier: 4.000A pdb=" N GLU A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.631A pdb=" N VAL A 351 " --> pdb=" O TRP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 381 Processing helix chain 'B' and resid 14 through 31 Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.613A pdb=" N GLU B 45 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 46 " --> pdb=" O HIS B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.765A pdb=" N ASN B 140 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'C' and resid 8 through 16 removed outlier: 4.362A pdb=" N GLU C 16 " --> pdb=" O PHE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 129 through 135 removed outlier: 4.434A pdb=" N GLN C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 149 Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.640A pdb=" N GLY D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'E' and resid 33 through 38 removed outlier: 3.682A pdb=" N THR E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 66 through 84 Processing helix chain 'E' and resid 96 through 111 removed outlier: 4.407A pdb=" N LEU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 22 removed outlier: 3.809A pdb=" N TYR F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 65 through 78 removed outlier: 3.821A pdb=" N LYS F 76 " --> pdb=" O HIS F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 111 Processing helix chain 'F' and resid 128 through 140 Processing helix chain 'F' and resid 153 through 165 removed outlier: 3.728A pdb=" N VAL F 165 " --> pdb=" O TRP F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 194 Processing helix chain 'F' and resid 198 through 207 removed outlier: 3.965A pdb=" N ASN F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 266 Processing helix chain 'F' and resid 267 through 270 Processing helix chain 'F' and resid 288 through 302 Processing helix chain 'F' and resid 320 through 332 removed outlier: 3.547A pdb=" N GLY F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 351 removed outlier: 3.654A pdb=" N VAL F 351 " --> pdb=" O TRP F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 381 removed outlier: 3.567A pdb=" N ASN F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 31 Processing helix chain 'G' and resid 32 through 36 removed outlier: 4.288A pdb=" N ALA G 35 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 109 Processing helix chain 'G' and resid 118 through 126 Processing helix chain 'G' and resid 135 through 140 removed outlier: 3.949A pdb=" N ASN G 140 " --> pdb=" O ALA G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 154 Processing helix chain 'G' and resid 165 through 170 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 36 through 51 Processing helix chain 'H' and resid 129 through 135 removed outlier: 4.411A pdb=" N GLN H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 147 Processing helix chain 'I' and resid 23 through 36 removed outlier: 3.573A pdb=" N GLY I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE I 34 " --> pdb=" O ILE I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 61 Processing helix chain 'J' and resid 33 through 38 removed outlier: 3.836A pdb=" N THR J 38 " --> pdb=" O GLU J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 46 Processing helix chain 'J' and resid 66 through 83 Processing helix chain 'J' and resid 96 through 111 removed outlier: 4.168A pdb=" N LEU J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 54 removed outlier: 3.720A pdb=" N ASP A 50 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TRP A 94 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR A 148 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 116 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LYS A 150 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE A 118 " --> pdb=" O LYS A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 231 through 243 removed outlier: 5.144A pdb=" N VAL A 224 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N GLN A 237 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N TYR A 222 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N ARG A 239 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 11.769A pdb=" N LEU A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.819A pdb=" N ASP C 120 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.746A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR B 68 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 13 Processing sheet with id=AA6, first strand: chain 'D' and resid 43 through 45 removed outlier: 3.865A pdb=" N ALA D 73 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 75 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 8 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 77 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 15 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYS E 32 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP D 17 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS E 27 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL E 60 " --> pdb=" O TYR E 18 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 8 through 9 removed outlier: 3.732A pdb=" N ASP F 50 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 231 through 243 removed outlier: 8.903A pdb=" N LEU F 234 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N HIS F 228 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N ASN F 236 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 11.642A pdb=" N ARG F 226 " --> pdb=" O ASN F 236 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG F 238 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR F 219 " --> pdb=" O SER F 284 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER F 284 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TRP F 285 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS F 334 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 5 through 9 removed outlier: 3.643A pdb=" N ASP H 120 " --> pdb=" O ASP H 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR H 85 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.837A pdb=" N VAL G 13 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN G 83 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU G 64 " --> pdb=" O HIS G 56 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N HIS G 56 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE G 66 " --> pdb=" O GLU G 54 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU G 54 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR G 68 " --> pdb=" O SER G 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.837A pdb=" N VAL G 13 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN G 83 " --> pdb=" O VAL G 13 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 12 through 18 removed outlier: 4.119A pdb=" N ALA I 73 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET I 6 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL I 75 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG I 8 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU I 77 " --> pdb=" O ARG I 8 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU I 44 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 28 through 32 668 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2590 1.32 - 1.45: 4479 1.45 - 1.57: 8253 1.57 - 1.69: 34 1.69 - 1.81: 134 Bond restraints: 15490 Sorted by residual: bond pdb=" CA ASP G 104 " pdb=" C ASP G 104 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.32e-02 5.74e+03 1.43e+01 bond pdb=" CA HIS B 80 " pdb=" C HIS B 80 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.26e-02 6.30e+03 1.12e+01 bond pdb=" CA TRP G 70 " pdb=" C TRP G 70 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" CA THR B 20 " pdb=" C THR B 20 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.29e-02 6.01e+03 8.51e+00 bond pdb=" C ASP G 104 " pdb=" O ASP G 104 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.22e-02 6.72e+03 8.31e+00 ... (remaining 15485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 20278 1.33 - 2.66: 570 2.66 - 3.99: 137 3.99 - 5.33: 33 5.33 - 6.66: 3 Bond angle restraints: 21021 Sorted by residual: angle pdb=" N HIS B 80 " pdb=" CA HIS B 80 " pdb=" C HIS B 80 " ideal model delta sigma weight residual 111.14 105.94 5.20 1.08e+00 8.57e-01 2.32e+01 angle pdb=" N THR G 74 " pdb=" CA THR G 74 " pdb=" C THR G 74 " ideal model delta sigma weight residual 111.28 106.41 4.87 1.09e+00 8.42e-01 2.00e+01 angle pdb=" N GLU B 76 " pdb=" CA GLU B 76 " pdb=" C GLU B 76 " ideal model delta sigma weight residual 110.43 115.76 -5.33 1.31e+00 5.83e-01 1.66e+01 angle pdb=" C ILE F 266 " pdb=" CA ILE F 266 " pdb=" CB ILE F 266 " ideal model delta sigma weight residual 113.70 109.87 3.83 9.50e-01 1.11e+00 1.63e+01 angle pdb=" N TRP B 174 " pdb=" CA TRP B 174 " pdb=" C TRP B 174 " ideal model delta sigma weight residual 111.36 115.66 -4.30 1.09e+00 8.42e-01 1.56e+01 ... (remaining 21016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 8217 17.83 - 35.65: 741 35.65 - 53.48: 179 53.48 - 71.31: 46 71.31 - 89.14: 20 Dihedral angle restraints: 9203 sinusoidal: 4035 harmonic: 5168 Sorted by residual: dihedral pdb=" CA TYR B 110 " pdb=" C TYR B 110 " pdb=" N TYR B 111 " pdb=" CA TYR B 111 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLN F 168 " pdb=" C GLN F 168 " pdb=" N ARG F 169 " pdb=" CA ARG F 169 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA TYR G 110 " pdb=" C TYR G 110 " pdb=" N TYR G 111 " pdb=" CA TYR G 111 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 9200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1758 0.045 - 0.090: 291 0.090 - 0.135: 121 0.135 - 0.180: 11 0.180 - 0.225: 2 Chirality restraints: 2183 Sorted by residual: chirality pdb=" CA PHE A 206 " pdb=" N PHE A 206 " pdb=" C PHE A 206 " pdb=" CB PHE A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C3' A K 3 " pdb=" C4' A K 3 " pdb=" O3' A K 3 " pdb=" C2' A K 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA VAL G 85 " pdb=" N VAL G 85 " pdb=" C VAL G 85 " pdb=" CB VAL G 85 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 2180 not shown) Planarity restraints: 2639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 76 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C GLU B 76 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU B 76 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG B 77 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 103 " 0.012 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ALA G 103 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA G 103 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP G 104 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 79 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C TRP B 79 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP B 79 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 80 " -0.013 2.00e-02 2.50e+03 ... (remaining 2636 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3437 2.79 - 3.32: 14109 3.32 - 3.85: 23897 3.85 - 4.37: 28511 4.37 - 4.90: 48814 Nonbonded interactions: 118768 Sorted by model distance: nonbonded pdb=" OH TYR E 79 " pdb=" O PRO E 91 " model vdw 2.264 3.040 nonbonded pdb=" OE2 GLU F 191 " pdb=" OH TYR F 222 " model vdw 2.271 3.040 nonbonded pdb=" N GLU E 64 " pdb=" OE1 GLU E 64 " model vdw 2.272 3.120 nonbonded pdb=" OG1 THR I 23 " pdb=" O LYS I 55 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN F 57 " pdb=" OH TYR F 59 " model vdw 2.305 3.040 ... (remaining 118763 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 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = (chain 'H' and resid 7 through 156) } ncs_group { reference = (chain 'D' and (resid 2 through 80 or resid 89 through 96)) selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 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: 0.040 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.160 Find NCS groups from input model: 0.150 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 0.050 15510 Z= 0.205 Angle : 0.575 6.657 21025 Z= 0.334 Chirality : 0.041 0.225 2183 Planarity : 0.005 0.065 2639 Dihedral : 15.035 89.136 5851 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.64 (0.20), residues: 1728 helix: 1.69 (0.21), residues: 599 sheet: -0.27 (0.28), residues: 336 loop : -0.16 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 41 TYR 0.017 0.001 TYR J 79 PHE 0.013 0.001 PHE A 206 TRP 0.015 0.001 TRP C 113 HIS 0.008 0.001 HIS J 27 Details of bonding type rmsd covalent geometry : bond 0.00357 (15490) covalent geometry : angle 0.57328 (21021) hydrogen bonds : bond 0.14364 ( 662) hydrogen bonds : angle 6.04121 ( 1902) metal coordination : bond 0.00417 ( 20) metal coordination : angle 3.53846 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 277 time to evaluate : 0.463 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 THR cc_start: 0.8612 (p) cc_final: 0.8355 (p) REVERT: E 74 CYS cc_start: 0.7224 (m) cc_final: 0.6858 (m) REVERT: E 77 PHE cc_start: 0.8233 (m-10) cc_final: 0.7953 (m-80) REVERT: F 219 TYR cc_start: 0.7259 (m-80) cc_final: 0.7056 (m-10) REVERT: F 285 TRP cc_start: 0.6895 (m100) cc_final: 0.6644 (m100) REVERT: G 1 MET cc_start: 0.6735 (ppp) cc_final: 0.6363 (ppp) REVERT: G 99 ASP cc_start: 0.8225 (t0) cc_final: 0.7817 (t70) REVERT: G 168 LYS cc_start: 0.8654 (tmtt) cc_final: 0.8232 (tptp) REVERT: H 11 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8371 (mmtt) REVERT: H 122 MET cc_start: 0.8513 (mtt) cc_final: 0.7645 (mtm) REVERT: J 105 MET cc_start: 0.4214 (mmt) cc_final: 0.3863 (mmp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.1513 time to fit residues: 58.0872 Evaluate side-chains 165 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 HIS E 61 ASN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS G 105 GLN H 41 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.098531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.069767 restraints weight = 58404.817| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 4.63 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 15510 Z= 0.257 Angle : 0.658 7.393 21025 Z= 0.344 Chirality : 0.044 0.168 2183 Planarity : 0.005 0.066 2639 Dihedral : 8.026 60.319 2198 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.33 % Allowed : 9.42 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.55 (0.20), residues: 1728 helix: 1.54 (0.21), residues: 622 sheet: -0.43 (0.27), residues: 357 loop : -0.12 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 82 TYR 0.017 0.002 TYR B 135 PHE 0.020 0.002 PHE C 32 TRP 0.018 0.002 TRP A 94 HIS 0.006 0.001 HIS J 27 Details of bonding type rmsd covalent geometry : bond 0.00574 (15490) covalent geometry : angle 0.65467 (21021) hydrogen bonds : bond 0.04324 ( 662) hydrogen bonds : angle 5.29197 ( 1902) metal coordination : bond 0.01064 ( 20) metal coordination : angle 4.75219 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.575 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 17 MET cc_start: 0.1884 (mpp) cc_final: 0.1468 (pmm) REVERT: E 70 LEU cc_start: 0.9018 (tt) cc_final: 0.8634 (tp) REVERT: E 74 CYS cc_start: 0.8004 (m) cc_final: 0.7487 (m) REVERT: F 219 TYR cc_start: 0.7667 (m-80) cc_final: 0.7224 (m-10) REVERT: F 259 GLU cc_start: 0.7781 (mp0) cc_final: 0.7516 (pm20) REVERT: F 285 TRP cc_start: 0.6824 (m100) cc_final: 0.6539 (m100) REVERT: G 1 MET cc_start: 0.7613 (ppp) cc_final: 0.7175 (ppp) REVERT: G 54 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8352 (tt0) REVERT: G 101 GLU cc_start: 0.9034 (mp0) cc_final: 0.8776 (mp0) REVERT: G 168 LYS cc_start: 0.9117 (tmtt) cc_final: 0.8667 (tptp) REVERT: J 105 MET cc_start: 0.4520 (mmt) cc_final: 0.4267 (mmp) outliers start: 21 outliers final: 12 residues processed: 185 average time/residue: 0.1292 time to fit residues: 35.4565 Evaluate side-chains 169 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 93 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 HIS ** J 108 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 = 0.4111 r_free = 0.4111 target = 0.100054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.069909 restraints weight = 58663.921| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 4.77 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15510 Z= 0.113 Angle : 0.577 8.509 21025 Z= 0.296 Chirality : 0.041 0.198 2183 Planarity : 0.004 0.053 2639 Dihedral : 7.734 59.496 2198 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.58 % Allowed : 10.56 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.89 (0.21), residues: 1728 helix: 1.77 (0.22), residues: 622 sheet: -0.19 (0.26), residues: 377 loop : 0.11 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 68 TYR 0.015 0.001 TYR E 79 PHE 0.051 0.001 PHE E 77 TRP 0.023 0.002 TRP A 211 HIS 0.012 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00251 (15490) covalent geometry : angle 0.57449 (21021) hydrogen bonds : bond 0.03348 ( 662) hydrogen bonds : angle 4.92747 ( 1902) metal coordination : bond 0.00418 ( 20) metal coordination : angle 3.84502 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 ASP cc_start: 0.8467 (p0) cc_final: 0.8228 (p0) REVERT: C 136 ASP cc_start: 0.8324 (t0) cc_final: 0.7684 (t0) REVERT: D 80 ARG cc_start: 0.6778 (ttp-170) cc_final: 0.6533 (mmp-170) REVERT: E 17 MET cc_start: 0.2070 (mpp) cc_final: 0.1707 (pmm) REVERT: E 70 LEU cc_start: 0.9140 (tt) cc_final: 0.8839 (tt) REVERT: E 74 CYS cc_start: 0.7610 (m) cc_final: 0.7243 (m) REVERT: E 104 LEU cc_start: 0.8995 (tp) cc_final: 0.8736 (mt) REVERT: F 219 TYR cc_start: 0.7474 (m-80) cc_final: 0.7169 (m-10) REVERT: F 259 GLU cc_start: 0.7731 (mp0) cc_final: 0.7431 (pm20) REVERT: G 1 MET cc_start: 0.7361 (ppp) cc_final: 0.6840 (ppp) REVERT: G 101 GLU cc_start: 0.9038 (mp0) cc_final: 0.8773 (mp0) REVERT: G 168 LYS cc_start: 0.9129 (tmtt) cc_final: 0.8689 (tptp) REVERT: H 64 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6671 (tp) outliers start: 25 outliers final: 14 residues processed: 195 average time/residue: 0.1156 time to fit residues: 33.8393 Evaluate side-chains 173 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 120 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 161 optimal weight: 50.0000 chunk 138 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 126 optimal weight: 0.7980 chunk 54 optimal weight: 0.8980 chunk 139 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 HIS J 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.099554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.069373 restraints weight = 58345.494| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.76 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15510 Z= 0.117 Angle : 0.556 11.500 21025 Z= 0.283 Chirality : 0.040 0.182 2183 Planarity : 0.004 0.047 2639 Dihedral : 7.595 59.465 2198 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.83 % Allowed : 12.14 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.92 (0.21), residues: 1728 helix: 1.73 (0.21), residues: 628 sheet: -0.08 (0.26), residues: 391 loop : 0.12 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 68 TYR 0.015 0.001 TYR B 147 PHE 0.016 0.001 PHE D 15 TRP 0.022 0.001 TRP F 285 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00264 (15490) covalent geometry : angle 0.55391 (21021) hydrogen bonds : bond 0.03111 ( 662) hydrogen bonds : angle 4.72336 ( 1902) metal coordination : bond 0.00516 ( 20) metal coordination : angle 3.35275 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.669 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7966 (mmm) cc_final: 0.7330 (mmm) REVERT: A 338 MET cc_start: 0.9033 (mmm) cc_final: 0.8767 (mmm) REVERT: D 44 LEU cc_start: 0.8953 (mp) cc_final: 0.8604 (mt) REVERT: E 104 LEU cc_start: 0.9020 (tp) cc_final: 0.8736 (mt) REVERT: F 219 TYR cc_start: 0.7490 (m-80) cc_final: 0.7193 (m-10) REVERT: F 259 GLU cc_start: 0.7859 (mp0) cc_final: 0.7556 (pm20) REVERT: G 1 MET cc_start: 0.7383 (ppp) cc_final: 0.6804 (ppp) REVERT: G 8 MET cc_start: 0.9144 (mmm) cc_final: 0.8866 (tpp) REVERT: G 168 LYS cc_start: 0.9125 (tmtt) cc_final: 0.8691 (tptp) REVERT: H 64 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6649 (tp) outliers start: 29 outliers final: 22 residues processed: 192 average time/residue: 0.1149 time to fit residues: 33.7944 Evaluate side-chains 182 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain J residue 108 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 12 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 GLN F 140 GLN J 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.099948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.069879 restraints weight = 58394.398| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 4.57 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15510 Z= 0.105 Angle : 0.547 9.880 21025 Z= 0.278 Chirality : 0.040 0.177 2183 Planarity : 0.004 0.050 2639 Dihedral : 7.493 59.354 2198 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.09 % Allowed : 12.45 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.86 (0.21), residues: 1728 helix: 1.70 (0.21), residues: 630 sheet: -0.18 (0.25), residues: 386 loop : 0.12 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 68 TYR 0.015 0.001 TYR B 147 PHE 0.037 0.001 PHE F 262 TRP 0.022 0.001 TRP A 211 HIS 0.004 0.001 HIS G 56 Details of bonding type rmsd covalent geometry : bond 0.00235 (15490) covalent geometry : angle 0.54529 (21021) hydrogen bonds : bond 0.03017 ( 662) hydrogen bonds : angle 4.61777 ( 1902) metal coordination : bond 0.00393 ( 20) metal coordination : angle 3.20396 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 0.498 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8059 (mmm) cc_final: 0.7224 (mmm) REVERT: A 268 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.7713 (t80) REVERT: D 44 LEU cc_start: 0.8894 (mp) cc_final: 0.8492 (mt) REVERT: E 104 LEU cc_start: 0.9058 (tp) cc_final: 0.8744 (mt) REVERT: F 219 TYR cc_start: 0.7506 (m-80) cc_final: 0.7252 (m-10) REVERT: F 259 GLU cc_start: 0.7878 (mp0) cc_final: 0.7560 (pm20) REVERT: G 1 MET cc_start: 0.7649 (ppp) cc_final: 0.7091 (ppp) REVERT: G 101 GLU cc_start: 0.8882 (mp0) cc_final: 0.8633 (pm20) REVERT: G 168 LYS cc_start: 0.9136 (tmtt) cc_final: 0.8711 (tptp) REVERT: H 64 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6568 (tp) outliers start: 33 outliers final: 20 residues processed: 186 average time/residue: 0.1017 time to fit residues: 29.2477 Evaluate side-chains 175 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 0.0980 chunk 43 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN G 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.099528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.069495 restraints weight = 58407.482| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 4.70 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15510 Z= 0.119 Angle : 0.561 13.286 21025 Z= 0.283 Chirality : 0.040 0.180 2183 Planarity : 0.004 0.049 2639 Dihedral : 7.470 59.292 2198 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.28 % Allowed : 12.58 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.94 (0.21), residues: 1728 helix: 1.75 (0.22), residues: 630 sheet: -0.12 (0.25), residues: 400 loop : 0.17 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 68 TYR 0.011 0.001 TYR B 147 PHE 0.048 0.001 PHE E 77 TRP 0.045 0.001 TRP F 361 HIS 0.006 0.001 HIS G 48 Details of bonding type rmsd covalent geometry : bond 0.00272 (15490) covalent geometry : angle 0.55953 (21021) hydrogen bonds : bond 0.03044 ( 662) hydrogen bonds : angle 4.58476 ( 1902) metal coordination : bond 0.00498 ( 20) metal coordination : angle 3.26113 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 0.570 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7777 (t80) REVERT: A 338 MET cc_start: 0.8996 (mmm) cc_final: 0.8566 (mmm) REVERT: B 14 ASP cc_start: 0.8789 (p0) cc_final: 0.8260 (p0) REVERT: B 70 TRP cc_start: 0.7801 (OUTLIER) cc_final: 0.7501 (m-10) REVERT: E 104 LEU cc_start: 0.9069 (tp) cc_final: 0.8744 (mt) REVERT: F 219 TYR cc_start: 0.7520 (m-80) cc_final: 0.7245 (m-10) REVERT: F 259 GLU cc_start: 0.7858 (mp0) cc_final: 0.7517 (pm20) REVERT: G 1 MET cc_start: 0.7683 (ppp) cc_final: 0.7125 (ppp) REVERT: G 168 LYS cc_start: 0.9136 (tmtt) cc_final: 0.8716 (tptp) REVERT: H 28 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7625 (mppt) outliers start: 36 outliers final: 25 residues processed: 188 average time/residue: 0.1139 time to fit residues: 32.5863 Evaluate side-chains 184 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 16 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 0.9980 chunk 167 optimal weight: 20.0000 chunk 2 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 147 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN F 140 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.098827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.068589 restraints weight = 58291.523| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 4.84 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15510 Z= 0.140 Angle : 0.586 14.802 21025 Z= 0.292 Chirality : 0.040 0.184 2183 Planarity : 0.004 0.048 2639 Dihedral : 7.471 59.218 2198 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.21 % Allowed : 13.72 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.87 (0.21), residues: 1728 helix: 1.73 (0.22), residues: 630 sheet: -0.20 (0.27), residues: 363 loop : 0.10 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 68 TYR 0.020 0.001 TYR B 147 PHE 0.025 0.001 PHE H 18 TRP 0.028 0.001 TRP F 361 HIS 0.009 0.001 HIS G 48 Details of bonding type rmsd covalent geometry : bond 0.00321 (15490) covalent geometry : angle 0.58395 (21021) hydrogen bonds : bond 0.03107 ( 662) hydrogen bonds : angle 4.58651 ( 1902) metal coordination : bond 0.00581 ( 20) metal coordination : angle 3.36460 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.602 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7709 (mmm) cc_final: 0.7063 (mmm) REVERT: A 268 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.7759 (t80) REVERT: A 338 MET cc_start: 0.9024 (mmm) cc_final: 0.8609 (mmm) REVERT: B 14 ASP cc_start: 0.8761 (p0) cc_final: 0.8268 (p0) REVERT: B 70 TRP cc_start: 0.7858 (OUTLIER) cc_final: 0.7498 (m-10) REVERT: B 78 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7909 (t70) REVERT: E 104 LEU cc_start: 0.9077 (tp) cc_final: 0.8732 (mt) REVERT: F 219 TYR cc_start: 0.7559 (m-80) cc_final: 0.7277 (m-10) REVERT: F 259 GLU cc_start: 0.7890 (mp0) cc_final: 0.7553 (pm20) REVERT: G 1 MET cc_start: 0.7602 (ppp) cc_final: 0.7027 (ppp) REVERT: G 168 LYS cc_start: 0.9122 (tmtt) cc_final: 0.8703 (tptp) REVERT: H 28 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7673 (mppt) REVERT: H 98 LYS cc_start: 0.9130 (tttt) cc_final: 0.8875 (ttmt) outliers start: 35 outliers final: 27 residues processed: 186 average time/residue: 0.1132 time to fit residues: 31.9250 Evaluate side-chains 185 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 0.0030 chunk 61 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 165 optimal weight: 30.0000 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN F 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.099249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.069129 restraints weight = 58954.453| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 4.88 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15510 Z= 0.113 Angle : 0.577 14.156 21025 Z= 0.286 Chirality : 0.040 0.180 2183 Planarity : 0.004 0.050 2639 Dihedral : 7.422 59.595 2198 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.02 % Allowed : 14.48 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.91 (0.21), residues: 1728 helix: 1.74 (0.22), residues: 632 sheet: -0.22 (0.27), residues: 370 loop : 0.18 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 93 TYR 0.015 0.001 TYR B 147 PHE 0.051 0.001 PHE E 77 TRP 0.028 0.001 TRP A 211 HIS 0.006 0.001 HIS G 48 Details of bonding type rmsd covalent geometry : bond 0.00259 (15490) covalent geometry : angle 0.57587 (21021) hydrogen bonds : bond 0.02935 ( 662) hydrogen bonds : angle 4.52770 ( 1902) metal coordination : bond 0.00467 ( 20) metal coordination : angle 2.75466 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7846 (mmm) cc_final: 0.7151 (mmm) REVERT: A 268 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7718 (t80) REVERT: A 338 MET cc_start: 0.9008 (mmm) cc_final: 0.8576 (mmm) REVERT: B 14 ASP cc_start: 0.8792 (p0) cc_final: 0.8337 (p0) REVERT: B 70 TRP cc_start: 0.7771 (OUTLIER) cc_final: 0.7482 (m-10) REVERT: B 78 ASP cc_start: 0.8149 (OUTLIER) cc_final: 0.7915 (t70) REVERT: E 104 LEU cc_start: 0.9081 (tp) cc_final: 0.8731 (mt) REVERT: F 139 CYS cc_start: 0.8395 (m) cc_final: 0.7988 (m) REVERT: F 219 TYR cc_start: 0.7526 (m-80) cc_final: 0.7276 (m-10) REVERT: F 259 GLU cc_start: 0.7868 (mp0) cc_final: 0.7521 (pm20) REVERT: F 277 TYR cc_start: 0.8028 (m-80) cc_final: 0.7723 (m-80) REVERT: G 1 MET cc_start: 0.7700 (ppp) cc_final: 0.7129 (ppp) REVERT: G 168 LYS cc_start: 0.9108 (tmtt) cc_final: 0.8690 (tptp) REVERT: H 28 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7598 (mppt) outliers start: 32 outliers final: 22 residues processed: 186 average time/residue: 0.1234 time to fit residues: 34.2760 Evaluate side-chains 182 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 156 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 103 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 8.9990 chunk 12 optimal weight: 0.7980 chunk 147 optimal weight: 30.0000 chunk 40 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN G 105 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.098615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.068466 restraints weight = 59132.778| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 4.89 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15510 Z= 0.145 Angle : 0.598 13.750 21025 Z= 0.298 Chirality : 0.041 0.176 2183 Planarity : 0.004 0.049 2639 Dihedral : 7.450 59.107 2198 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.09 % Allowed : 14.54 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.89 (0.21), residues: 1728 helix: 1.73 (0.22), residues: 632 sheet: -0.18 (0.27), residues: 363 loop : 0.11 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.022 0.001 TYR B 147 PHE 0.018 0.001 PHE H 18 TRP 0.058 0.001 TRP F 361 HIS 0.005 0.001 HIS G 48 Details of bonding type rmsd covalent geometry : bond 0.00331 (15490) covalent geometry : angle 0.59701 (21021) hydrogen bonds : bond 0.03115 ( 662) hydrogen bonds : angle 4.57925 ( 1902) metal coordination : bond 0.00601 ( 20) metal coordination : angle 3.06349 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.560 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8037 (mmm) cc_final: 0.7539 (mmm) REVERT: A 268 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7728 (t80) REVERT: B 14 ASP cc_start: 0.8808 (p0) cc_final: 0.8361 (p0) REVERT: B 70 TRP cc_start: 0.7856 (OUTLIER) cc_final: 0.7475 (m-10) REVERT: E 104 LEU cc_start: 0.9079 (tp) cc_final: 0.8729 (mt) REVERT: F 139 CYS cc_start: 0.8524 (m) cc_final: 0.8147 (m) REVERT: F 277 TYR cc_start: 0.7991 (m-80) cc_final: 0.7687 (m-80) REVERT: F 338 MET cc_start: 0.5819 (mpp) cc_final: 0.4430 (mpp) REVERT: G 1 MET cc_start: 0.7700 (ppp) cc_final: 0.7117 (ppp) REVERT: G 168 LYS cc_start: 0.9112 (tmtt) cc_final: 0.8703 (tptp) REVERT: H 28 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7629 (mppt) outliers start: 33 outliers final: 26 residues processed: 181 average time/residue: 0.1118 time to fit residues: 30.5392 Evaluate side-chains 185 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 156 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 77 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 87 optimal weight: 0.0970 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.099136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.070952 restraints weight = 58677.985| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 4.57 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15510 Z= 0.114 Angle : 0.598 14.933 21025 Z= 0.294 Chirality : 0.040 0.145 2183 Planarity : 0.004 0.047 2639 Dihedral : 7.413 59.047 2198 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.77 % Allowed : 15.17 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.91 (0.21), residues: 1728 helix: 1.74 (0.22), residues: 632 sheet: -0.20 (0.27), residues: 369 loop : 0.16 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 68 TYR 0.020 0.001 TYR B 147 PHE 0.053 0.001 PHE E 77 TRP 0.042 0.001 TRP F 361 HIS 0.005 0.001 HIS G 48 Details of bonding type rmsd covalent geometry : bond 0.00263 (15490) covalent geometry : angle 0.59651 (21021) hydrogen bonds : bond 0.02929 ( 662) hydrogen bonds : angle 4.51959 ( 1902) metal coordination : bond 0.00455 ( 20) metal coordination : angle 2.68165 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.592 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8252 (mmm) cc_final: 0.7768 (mmm) REVERT: A 268 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7745 (t80) REVERT: B 70 TRP cc_start: 0.7803 (OUTLIER) cc_final: 0.7484 (m-10) REVERT: E 104 LEU cc_start: 0.9015 (tp) cc_final: 0.8670 (mt) REVERT: F 139 CYS cc_start: 0.8819 (m) cc_final: 0.8103 (m) REVERT: F 259 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: F 277 TYR cc_start: 0.8027 (m-80) cc_final: 0.7640 (m-80) REVERT: F 338 MET cc_start: 0.5831 (mpp) cc_final: 0.4518 (mpp) REVERT: G 1 MET cc_start: 0.7982 (ppp) cc_final: 0.7441 (ppp) REVERT: G 168 LYS cc_start: 0.9132 (tmtt) cc_final: 0.8724 (tptp) REVERT: H 28 LYS cc_start: 0.7830 (OUTLIER) cc_final: 0.7455 (mppt) outliers start: 28 outliers final: 22 residues processed: 178 average time/residue: 0.1126 time to fit residues: 30.5621 Evaluate side-chains 183 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 146 GLN Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 259 GLU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 168 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 68 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.099052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.070832 restraints weight = 58619.909| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.55 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15510 Z= 0.124 Angle : 0.606 15.037 21025 Z= 0.300 Chirality : 0.040 0.164 2183 Planarity : 0.004 0.045 2639 Dihedral : 7.407 59.024 2198 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.77 % Allowed : 15.17 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.91 (0.21), residues: 1728 helix: 1.71 (0.21), residues: 632 sheet: -0.19 (0.27), residues: 369 loop : 0.18 (0.24), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 313 TYR 0.019 0.001 TYR B 147 PHE 0.017 0.001 PHE E 77 TRP 0.044 0.001 TRP F 361 HIS 0.006 0.001 HIS B 80 Details of bonding type rmsd covalent geometry : bond 0.00286 (15490) covalent geometry : angle 0.60505 (21021) hydrogen bonds : bond 0.02954 ( 662) hydrogen bonds : angle 4.51902 ( 1902) metal coordination : bond 0.00497 ( 20) metal coordination : angle 2.59611 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3959.25 seconds wall clock time: 68 minutes 25.06 seconds (4105.06 seconds total)