Starting phenix.real_space_refine on Sat Sep 12 10:01:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cx2_27034/09_2026/8cx2_27034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cx2_27034/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8cx2_27034/09_2026/8cx2_27034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cx2_27034/09_2026/8cx2_27034.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8cx2_27034/09_2026/8cx2_27034.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cx2_27034/09_2026/8cx2_27034.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cx2_27034/09_2026/8cx2_27034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cx2_27034/09_2026/8cx2_27034.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 3.05, per 1000 atoms: 0.20 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: 1.09 Conformation dependent library (CDL) restraints added in 588.7 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: 1.20 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: 2.11 Time building geometry restraints manager: 1.36 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: 20163 1.33 - 2.66: 628 2.66 - 3.99: 182 3.99 - 5.33: 45 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: 8143 17.83 - 35.65: 767 35.65 - 53.48: 173 53.48 - 71.31: 68 71.31 - 89.14: 28 Dihedral angle restraints: 9179 sinusoidal: 4011 harmonic: 5168 Sorted by residual: dihedral pdb=" C4' A L 5 " pdb=" C3' A L 5 " pdb=" C2' A L 5 " pdb=" C1' A L 5 " ideal model delta sinusoidal sigma weight residual 36.34 -36.09 72.43 1 3.10e+00 1.04e-01 6.97e+02 dihedral pdb=" C4' A K 5 " pdb=" C3' A K 5 " pdb=" C2' A K 5 " pdb=" C1' A K 5 " ideal model delta sinusoidal sigma weight residual 36.34 -35.78 72.13 1 3.10e+00 1.04e-01 6.92e+02 dihedral pdb=" C4' U L 6 " pdb=" C3' U L 6 " pdb=" C2' U L 6 " pdb=" C1' U L 6 " ideal model delta sinusoidal sigma weight residual 36.35 -35.40 71.75 1 3.10e+00 1.04e-01 6.86e+02 ... (remaining 9176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1841 0.056 - 0.113: 258 0.113 - 0.169: 44 0.169 - 0.226: 11 0.226 - 0.282: 29 Chirality restraints: 2183 Sorted by residual: chirality pdb=" C2' U L 6 " pdb=" C3' U L 6 " pdb=" O2' U L 6 " pdb=" C1' U L 6 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" C2' U K 6 " pdb=" C3' U K 6 " pdb=" O2' U K 6 " pdb=" C1' U K 6 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C2' A K 1 " pdb=" C3' A K 1 " pdb=" O2' A K 1 " pdb=" C1' A K 1 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.93e+00 ... (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: 2.690 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: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.570 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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= 0.207 Angle : 0.615 6.657 21025 Z= 0.345 Chirality : 0.052 0.282 2183 Planarity : 0.005 0.065 2639 Dihedral : 15.764 89.136 5827 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/Z covalent geometry : bond 0.00362 / 0.21 (15490) covalent geometry : angle 0.61329 / 0.35 (21021) hydrogen bonds : bond 0.14364 / 9.65 ( 662) hydrogen bonds : angle 6.04121 / 4.43 ( 1902) metal coordination : bond 0.00417 / 0.22 ( 20) metal coordination : angle 3.53846 / 1.98 ( 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 : 0.506 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: 0.1348 time to fit residues: 52.8974 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 : 0.554 ------------------------------------------------------------------------------- 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: 4.9990 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: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.098972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.068909 restraints weight = 58431.166| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 4.64 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15510 Z= 0.254 Angle : 0.785 11.438 21025 Z= 0.383 Chirality : 0.062 0.878 2183 Planarity : 0.005 0.067 2639 Dihedral : 9.892 139.493 2174 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.33 % Allowed : 9.17 % Favored : 89.51 % 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: 0.58 (0.20), residues: 1728 helix: 1.56 (0.21), residues: 622 sheet: -0.39 (0.27), residues: 357 loop : -0.11 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 69 TYR 0.016 0.002 TYR B 147 PHE 0.019 0.002 PHE C 32 TRP 0.022 0.002 TRP G 89 HIS 0.005 0.001 HIS J 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.25 (15490) covalent geometry : angle 0.78219 / 0.38 (21021) hydrogen bonds : bond 0.04299 / 2.81 ( 662) hydrogen bonds : angle 5.28312 / 3.84 ( 1902) metal coordination : bond 0.01126 / 0.68 ( 20) metal coordination : angle 4.66076 / 2.58 ( 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 : 0.614 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: 0.1946 (mpp) cc_final: 0.1496 (pmm) REVERT: E 38 THR cc_start: 0.8947 (p) cc_final: 0.8711 (p) REVERT: E 70 LEU cc_start: 0.9022 (tt) cc_final: 0.8708 (tp) REVERT: E 74 CYS cc_start: 0.7807 (m) cc_final: 0.7321 (m) REVERT: F 259 GLU cc_start: 0.7672 (mp0) cc_final: 0.7441 (pm20) REVERT: F 285 TRP cc_start: 0.6907 (m100) cc_final: 0.6627 (m100) REVERT: G 1 MET cc_start: 0.7268 (ppp) cc_final: 0.6802 (ppp) REVERT: G 101 GLU cc_start: 0.9028 (mp0) cc_final: 0.8771 (mp0) REVERT: G 168 LYS cc_start: 0.9125 (tmtt) cc_final: 0.8675 (tptp) REVERT: H 64 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6658 (tp) outliers start: 21 outliers final: 11 residues processed: 185 average time/residue: 0.1200 time to fit residues: 33.2890 Evaluate side-chains 168 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 3.9990 chunk 135 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 160 optimal weight: 0.0470 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.100162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.070338 restraints weight = 58589.126| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 4.72 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15510 Z= 0.128 Angle : 0.637 9.131 21025 Z= 0.319 Chirality : 0.049 0.516 2183 Planarity : 0.004 0.055 2639 Dihedral : 10.176 141.257 2174 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.58 % Allowed : 10.62 % Favored : 87.80 % 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: 1.75 (0.22), residues: 622 sheet: -0.20 (0.26), residues: 377 loop : 0.09 (0.24), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 68 TYR 0.021 0.001 TYR B 147 PHE 0.046 0.001 PHE E 77 TRP 0.034 0.002 TRP F 361 HIS 0.007 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (15490) covalent geometry : angle 0.63485 / 0.32 (21021) hydrogen bonds : bond 0.03432 / 2.26 ( 662) hydrogen bonds : angle 4.96224 / 3.60 ( 1902) metal coordination : bond 0.00515 / 0.32 ( 20) metal coordination : angle 4.00962 / 2.23 ( 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 202 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.735 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: B 14 ASP cc_start: 0.8421 (p0) cc_final: 0.8197 (p0) REVERT: C 136 ASP cc_start: 0.8405 (t0) cc_final: 0.7792 (t0) REVERT: E 17 MET cc_start: 0.1838 (mpp) cc_final: 0.1588 (pmm) REVERT: E 70 LEU cc_start: 0.9122 (tt) cc_final: 0.8805 (tp) REVERT: E 74 CYS cc_start: 0.7792 (m) cc_final: 0.7384 (m) REVERT: E 104 LEU cc_start: 0.8985 (tp) cc_final: 0.8726 (mt) REVERT: F 259 GLU cc_start: 0.7767 (mp0) cc_final: 0.7472 (pm20) REVERT: F 272 ASP cc_start: 0.7597 (t0) cc_final: 0.7396 (t70) REVERT: G 1 MET cc_start: 0.7184 (ppp) cc_final: 0.6641 (ppp) REVERT: G 101 GLU cc_start: 0.9047 (mp0) cc_final: 0.8763 (mp0) REVERT: G 168 LYS cc_start: 0.9126 (tmtt) cc_final: 0.8683 (tptp) REVERT: H 64 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6667 (tp) outliers start: 25 outliers final: 14 residues processed: 191 average time/residue: 0.1098 time to fit residues: 31.8076 Evaluate side-chains 172 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 23 SER 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: 0.0000 chunk 56 optimal weight: 10.0000 chunk 61 optimal weight: 0.0670 chunk 99 optimal weight: 0.8980 chunk 161 optimal weight: 50.0000 chunk 138 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 126 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 overall best weight: 1.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4111 r_free = 0.4111 target = 0.099611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.069593 restraints weight = 58474.315| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 4.84 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2829 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= 0.132 Angle : 0.611 11.632 21025 Z= 0.304 Chirality : 0.048 0.454 2183 Planarity : 0.004 0.046 2639 Dihedral : 10.065 141.996 2174 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.77 % Allowed : 12.14 % Favored : 86.09 % 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: 0.93 (0.21), residues: 1728 helix: 1.80 (0.22), residues: 622 sheet: -0.10 (0.26), residues: 391 loop : 0.11 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 313 TYR 0.015 0.001 TYR B 147 PHE 0.017 0.001 PHE D 15 TRP 0.025 0.001 TRP F 285 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (15490) covalent geometry : angle 0.60867 / 0.30 (21021) hydrogen bonds : bond 0.03170 / 2.10 ( 662) hydrogen bonds : angle 4.77758 / 3.48 ( 1902) metal coordination : bond 0.00559 / 0.37 ( 20) metal coordination : angle 4.12107 / 2.33 ( 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 199 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.595 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 268 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7592 (t80) REVERT: A 338 MET cc_start: 0.9041 (mmm) cc_final: 0.8787 (mmm) REVERT: E 104 LEU cc_start: 0.9031 (tp) cc_final: 0.8748 (mt) REVERT: F 259 GLU cc_start: 0.7856 (mp0) cc_final: 0.7561 (pm20) REVERT: F 272 ASP cc_start: 0.7653 (t0) cc_final: 0.7369 (t70) REVERT: G 1 MET cc_start: 0.7403 (ppp) cc_final: 0.6815 (ppp) REVERT: G 168 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8693 (tptp) REVERT: H 64 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6673 (tp) outliers start: 28 outliers final: 22 residues processed: 190 average time/residue: 0.1109 time to fit residues: 32.3276 Evaluate side-chains 184 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 21 LEU 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 63 ARG 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: 0.9980 chunk 42 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 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: 0.9990 chunk 25 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.099194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.069359 restraints weight = 59004.146| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 4.73 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15510 Z= 0.153 Angle : 0.614 10.252 21025 Z= 0.305 Chirality : 0.048 0.438 2183 Planarity : 0.004 0.049 2639 Dihedral : 10.040 142.299 2174 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.96 % Allowed : 13.08 % Favored : 84.96 % 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: 0.83 (0.21), residues: 1728 helix: 1.74 (0.22), residues: 630 sheet: -0.32 (0.26), residues: 365 loop : 0.08 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 68 TYR 0.017 0.001 TYR B 147 PHE 0.035 0.002 PHE F 262 TRP 0.046 0.002 TRP F 361 HIS 0.004 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15490) covalent geometry : angle 0.61175 / 0.30 (21021) hydrogen bonds : bond 0.03234 / 2.16 ( 662) hydrogen bonds : angle 4.71624 / 3.43 ( 1902) metal coordination : bond 0.00643 / 0.42 ( 20) metal coordination : angle 3.82186 / 2.14 ( 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 194 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.543 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: A 227 MET cc_start: 0.8006 (mmm) cc_final: 0.7230 (mmm) REVERT: A 268 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7607 (t80) REVERT: B 70 TRP cc_start: 0.7909 (OUTLIER) cc_final: 0.7536 (m-10) REVERT: B 78 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7636 (t0) REVERT: E 104 LEU cc_start: 0.9054 (tp) cc_final: 0.8756 (mt) REVERT: F 259 GLU cc_start: 0.7876 (mp0) cc_final: 0.7536 (pm20) REVERT: G 1 MET cc_start: 0.7337 (ppp) cc_final: 0.6749 (ppp) REVERT: G 101 GLU cc_start: 0.8901 (mp0) cc_final: 0.8635 (pm20) REVERT: G 168 LYS cc_start: 0.9127 (tmtt) cc_final: 0.8694 (tptp) REVERT: H 98 LYS cc_start: 0.9111 (tttt) cc_final: 0.8857 (ttmt) outliers start: 31 outliers final: 20 residues processed: 185 average time/residue: 0.1068 time to fit residues: 30.7844 Evaluate side-chains 173 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 74 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.099396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.069523 restraints weight = 58475.427| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.55 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15510 Z= 0.127 Angle : 0.616 13.986 21025 Z= 0.304 Chirality : 0.047 0.396 2183 Planarity : 0.004 0.051 2639 Dihedral : 10.008 142.677 2174 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.28 % Allowed : 13.15 % Favored : 84.58 % 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: 0.85 (0.21), residues: 1728 helix: 1.74 (0.22), residues: 630 sheet: -0.23 (0.26), residues: 384 loop : 0.08 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 68 TYR 0.012 0.001 TYR B 147 PHE 0.052 0.001 PHE E 77 TRP 0.028 0.001 TRP F 361 HIS 0.008 0.001 HIS G 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (15490) covalent geometry : angle 0.61442 / 0.30 (21021) hydrogen bonds : bond 0.03132 / 2.11 ( 662) hydrogen bonds : angle 4.64591 / 3.38 ( 1902) metal coordination : bond 0.00473 / 0.32 ( 20) metal coordination : angle 3.40923 / 1.92 ( 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 196 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 1.122 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: 0.8142 (mmm) cc_final: 0.7187 (mmm) REVERT: A 268 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7553 (t80) REVERT: B 14 ASP cc_start: 0.8769 (p0) cc_final: 0.8227 (p0) REVERT: B 70 TRP cc_start: 0.7864 (OUTLIER) cc_final: 0.7553 (m-10) REVERT: B 78 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7792 (t70) REVERT: E 104 LEU cc_start: 0.9033 (tp) cc_final: 0.8725 (mt) REVERT: F 259 GLU cc_start: 0.7891 (mp0) cc_final: 0.7540 (pm20) REVERT: G 1 MET cc_start: 0.7499 (ppp) cc_final: 0.6901 (ppp) REVERT: G 168 LYS cc_start: 0.9124 (tmtt) cc_final: 0.8695 (tptp) outliers start: 36 outliers final: 25 residues processed: 184 average time/residue: 0.1091 time to fit residues: 30.8247 Evaluate side-chains 177 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 149 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 80 HIS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 21 LEU 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 63 ARG 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 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: 7.9990 chunk 167 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 122 optimal weight: 0.3980 chunk 147 optimal weight: 0.8980 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.099558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.069646 restraints weight = 58681.796| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 5.20 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15510 Z= 0.121 Angle : 0.615 13.855 21025 Z= 0.302 Chirality : 0.046 0.359 2183 Planarity : 0.004 0.050 2639 Dihedral : 9.973 143.108 2174 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.96 % Allowed : 14.22 % Favored : 83.82 % 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: 1.75 (0.22), residues: 630 sheet: -0.21 (0.27), residues: 363 loop : 0.11 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 68 TYR 0.018 0.001 TYR B 147 PHE 0.031 0.001 PHE H 18 TRP 0.026 0.001 TRP A 211 HIS 0.012 0.001 HIS G 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (15490) covalent geometry : angle 0.61396 / 0.30 (21021) hydrogen bonds : bond 0.03024 / 2.04 ( 662) hydrogen bonds : angle 4.59072 / 3.34 ( 1902) metal coordination : bond 0.00477 / 0.32 ( 20) metal coordination : angle 3.15991 / 1.77 ( 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 195 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7770 (mmp80) REVERT: A 227 MET cc_start: 0.8178 (mmm) cc_final: 0.7345 (mmm) REVERT: A 268 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7569 (t80) REVERT: A 338 MET cc_start: 0.8984 (mmm) cc_final: 0.8575 (mmm) REVERT: B 14 ASP cc_start: 0.8710 (p0) cc_final: 0.8205 (p0) REVERT: B 70 TRP cc_start: 0.7824 (OUTLIER) cc_final: 0.7536 (m-10) REVERT: B 78 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7879 (t70) REVERT: D 44 LEU cc_start: 0.8980 (mp) cc_final: 0.8718 (mt) REVERT: E 104 LEU cc_start: 0.9029 (tp) cc_final: 0.8719 (mt) REVERT: F 259 GLU cc_start: 0.7879 (mp0) cc_final: 0.7519 (pm20) REVERT: G 1 MET cc_start: 0.7618 (ppp) cc_final: 0.7029 (ppp) REVERT: G 64 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8602 (tt) REVERT: G 168 LYS cc_start: 0.9120 (tmtt) cc_final: 0.8700 (tptp) REVERT: H 28 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7661 (mppt) outliers start: 31 outliers final: 24 residues processed: 185 average time/residue: 0.1050 time to fit residues: 29.8555 Evaluate side-chains 183 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG 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 80 HIS 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 G residue 23 SER Chi-restraints excluded: chain G residue 64 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 165 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4120 r_free = 0.4120 target = 0.099632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.069981 restraints weight = 58958.242| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 4.80 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3512 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= 0.113 Angle : 0.620 14.222 21025 Z= 0.302 Chirality : 0.046 0.311 2183 Planarity : 0.004 0.050 2639 Dihedral : 9.919 143.333 2174 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.21 % Allowed : 14.35 % Favored : 83.44 % 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: -0.21 (0.27), residues: 369 loop : 0.17 (0.23), residues: 727 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 0.051 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/Z covalent geometry : bond 0.00257 / 0.11 (15490) covalent geometry : angle 0.61893 / 0.30 (21021) hydrogen bonds : bond 0.02948 / 1.99 ( 662) hydrogen bonds : angle 4.51703 / 3.29 ( 1902) metal coordination : bond 0.00432 / 0.29 ( 20) metal coordination : angle 2.77284 / 1.53 ( 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 198 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 163 time to evaluate : 0.414 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 82 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7772 (mmp80) REVERT: A 227 MET cc_start: 0.8219 (mmm) cc_final: 0.7406 (mmm) REVERT: A 268 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7557 (t80) REVERT: A 338 MET cc_start: 0.8940 (mmm) cc_final: 0.8469 (mmm) REVERT: B 70 TRP cc_start: 0.7794 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: B 78 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7963 (t70) REVERT: D 44 LEU cc_start: 0.9039 (mp) cc_final: 0.8818 (mt) REVERT: E 104 LEU cc_start: 0.8992 (tp) cc_final: 0.8681 (mt) REVERT: F 259 GLU cc_start: 0.7895 (mp0) cc_final: 0.7537 (pm20) REVERT: G 1 MET cc_start: 0.7462 (ppp) cc_final: 0.6866 (ppp) REVERT: G 168 LYS cc_start: 0.9113 (tmtt) cc_final: 0.8694 (tptp) REVERT: H 28 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7755 (mppt) outliers start: 35 outliers final: 25 residues processed: 187 average time/residue: 0.1094 time to fit residues: 31.4559 Evaluate side-chains 185 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG 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 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 E residue 99 ILE Chi-restraints excluded: chain F residue 140 GLN 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 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 97 LEU 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: 4.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 147 optimal weight: 30.0000 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4110 r_free = 0.4110 target = 0.099013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.069244 restraints weight = 59443.809| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 5.24 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3598 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= 0.147 Angle : 0.637 13.429 21025 Z= 0.311 Chirality : 0.047 0.319 2183 Planarity : 0.004 0.048 2639 Dihedral : 9.936 144.833 2174 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.09 % Allowed : 14.66 % Favored : 83.25 % 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: 0.89 (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 0.006 0.000 ARG D 68 TYR 0.022 0.001 TYR B 147 PHE 0.020 0.001 PHE H 18 TRP 0.028 0.001 TRP A 211 HIS 0.005 0.001 HIS G 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (15490) covalent geometry : angle 0.63532 / 0.31 (21021) hydrogen bonds : bond 0.03120 / 2.10 ( 662) hydrogen bonds : angle 4.56733 / 3.32 ( 1902) metal coordination : bond 0.00600 / 0.39 ( 20) metal coordination : angle 2.94539 / 1.63 ( 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 : 0.594 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 268 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7582 (t80) REVERT: A 338 MET cc_start: 0.8962 (mmm) cc_final: 0.8754 (mmm) REVERT: B 14 ASP cc_start: 0.8787 (p0) cc_final: 0.8212 (p0) REVERT: B 70 TRP cc_start: 0.7855 (OUTLIER) cc_final: 0.7506 (m-10) REVERT: B 78 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7991 (t70) REVERT: F 139 CYS cc_start: 0.8547 (m) cc_final: 0.8221 (m) REVERT: F 259 GLU cc_start: 0.7865 (mp0) cc_final: 0.7504 (pm20) REVERT: F 338 MET cc_start: 0.5839 (mpp) cc_final: 0.4453 (mpp) REVERT: G 1 MET cc_start: 0.7639 (ppp) cc_final: 0.7046 (ppp) REVERT: G 64 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8618 (tt) REVERT: G 168 LYS cc_start: 0.9119 (tmtt) cc_final: 0.8709 (tptp) REVERT: H 28 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7653 (mppt) outliers start: 33 outliers final: 25 residues processed: 181 average time/residue: 0.1062 time to fit residues: 29.8976 Evaluate side-chains 187 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 80 HIS 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 140 GLN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 279 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 64 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain G residue 101 GLU 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: 6.9990 chunk 60 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 165 optimal weight: 0.0980 chunk 131 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 140 optimal weight: 8.9990 chunk 24 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 41 GLN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.099976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.070301 restraints weight = 58692.354| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 4.81 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15510 Z= 0.108 Angle : 0.643 14.528 21025 Z= 0.311 Chirality : 0.045 0.271 2183 Planarity : 0.004 0.047 2639 Dihedral : 9.896 143.488 2174 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.71 % Allowed : 15.55 % Favored : 82.74 % 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: -0.14 (0.27), residues: 358 loop : 0.11 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 142 TYR 0.018 0.001 TYR B 147 PHE 0.060 0.001 PHE E 77 TRP 0.059 0.002 TRP F 361 HIS 0.005 0.001 HIS G 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (15490) covalent geometry : angle 0.64220 / 0.31 (21021) hydrogen bonds : bond 0.02926 / 1.96 ( 662) hydrogen bonds : angle 4.50257 / 3.27 ( 1902) metal coordination : bond 0.00351 / 0.24 ( 20) metal coordination : angle 2.58451 / 1.41 ( 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 193 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.632 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 82 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7835 (mmp80) REVERT: A 227 MET cc_start: 0.7408 (mmm) cc_final: 0.7042 (mmm) REVERT: A 268 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7540 (t80) REVERT: A 338 MET cc_start: 0.8942 (mmm) cc_final: 0.8731 (mmm) REVERT: B 14 ASP cc_start: 0.8720 (p0) cc_final: 0.8131 (p0) REVERT: E 104 LEU cc_start: 0.9008 (tp) cc_final: 0.8701 (mt) REVERT: F 139 CYS cc_start: 0.8476 (m) cc_final: 0.8100 (m) REVERT: F 259 GLU cc_start: 0.7879 (mp0) cc_final: 0.7509 (pm20) REVERT: F 338 MET cc_start: 0.5734 (mpp) cc_final: 0.4439 (mpp) REVERT: G 1 MET cc_start: 0.7644 (ppp) cc_final: 0.7066 (ppp) REVERT: G 64 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8590 (tt) REVERT: G 168 LYS cc_start: 0.9149 (tmtt) cc_final: 0.8734 (tptp) REVERT: H 28 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7593 (mppt) REVERT: H 122 MET cc_start: 0.8179 (mmm) cc_final: 0.7670 (mmm) outliers start: 27 outliers final: 20 residues processed: 183 average time/residue: 0.1071 time to fit residues: 30.2561 Evaluate side-chains 181 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ARG Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 80 HIS 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 279 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 64 LEU 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: 9.9990 chunk 119 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 41 GLN F 140 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.097443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.069710 restraints weight = 59498.836| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 4.75 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15510 Z= 0.241 Angle : 0.702 13.834 21025 Z= 0.346 Chirality : 0.050 0.393 2183 Planarity : 0.004 0.049 2639 Dihedral : 10.067 148.855 2174 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.77 % Allowed : 15.61 % Favored : 82.62 % 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: 0.73 (0.21), residues: 1728 helix: 1.58 (0.21), residues: 632 sheet: -0.29 (0.27), residues: 363 loop : 0.06 (0.24), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 68 TYR 0.023 0.002 TYR B 147 PHE 0.030 0.002 PHE H 18 TRP 0.042 0.002 TRP F 361 HIS 0.006 0.001 HIS J 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (15490) covalent geometry : angle 0.69982 / 0.35 (21021) hydrogen bonds : bond 0.03591 / 2.42 ( 662) hydrogen bonds : angle 4.75927 / 3.45 ( 1902) metal coordination : bond 0.00897 / 0.56 ( 20) metal coordination : angle 3.78565 / 2.10 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3709.60 seconds wall clock time: 64 minutes 18.54 seconds (3858.54 seconds total)