Starting phenix.real_space_refine on Fri Jun 13 15:21:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cx2_27034/06_2025/8cx2_27034.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cx2_27034/06_2025/8cx2_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_27034/06_2025/8cx2_27034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cx2_27034/06_2025/8cx2_27034.map" model { file = "/net/cci-nas-00/data/ceres_data/8cx2_27034/06_2025/8cx2_27034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cx2_27034/06_2025/8cx2_27034.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15041 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3211 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain: "B" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1468 Classifications: {'peptide': 176} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 166} Chain: "C" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1254 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "D" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "F" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3211 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 19, 'TRANS': 357} Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1468 Classifications: {'peptide': 176} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 166} Chain: "H" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1275 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "I" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "K" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 4} Link IDs: {'rna2p': 4, 'rna3p': 4} Chain: "L" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2457 SG CYS A 288 34.823 21.522 36.834 1.00104.36 S ATOM 2480 SG CYS A 291 35.490 24.180 37.316 1.00 93.76 S ATOM 824 SG CYS A 97 55.944 55.618 50.636 1.00 46.37 S ATOM 846 SG CYS A 100 58.143 55.092 52.191 1.00 56.54 S ATOM 4195 SG CYS B 114 32.332 86.770 53.473 1.00 94.58 S ATOM 4339 SG CYS B 133 35.703 85.325 54.750 1.00 90.36 S ATOM 9776 SG CYS F 288 18.165 56.352 107.513 1.00132.85 S ATOM 9799 SG CYS F 291 21.029 56.636 106.539 1.00124.22 S ATOM 8143 SG CYS F 97 51.398 67.782 84.004 1.00 49.52 S ATOM 8165 SG CYS F 100 50.987 70.212 82.350 1.00 58.78 S ATOM 11514 SG CYS G 114 76.648 38.602 81.181 1.00162.59 S ATOM 11658 SG CYS G 133 75.213 41.532 79.251 1.00156.40 S Time building chain proxies: 9.11, per 1000 atoms: 0.61 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: 3.55 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.50 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: 3.99 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2590 1.32 - 1.45: 4479 1.45 - 1.57: 8253 1.57 - 1.69: 34 1.69 - 1.81: 134 Bond restraints: 15490 Sorted by residual: bond pdb=" CA ASP G 104 " pdb=" C ASP G 104 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.32e-02 5.74e+03 1.43e+01 bond pdb=" CA HIS B 80 " pdb=" C HIS B 80 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.26e-02 6.30e+03 1.12e+01 bond pdb=" CA TRP G 70 " pdb=" C TRP G 70 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" CA THR B 20 " pdb=" C THR B 20 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.29e-02 6.01e+03 8.51e+00 bond pdb=" C ASP G 104 " pdb=" O ASP G 104 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.22e-02 6.72e+03 8.31e+00 ... (remaining 15485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 20278 1.33 - 2.66: 570 2.66 - 3.99: 137 3.99 - 5.33: 33 5.33 - 6.66: 3 Bond angle restraints: 21021 Sorted by residual: angle pdb=" N HIS B 80 " pdb=" CA HIS B 80 " pdb=" C HIS B 80 " ideal model delta sigma weight residual 111.14 105.94 5.20 1.08e+00 8.57e-01 2.32e+01 angle pdb=" N THR G 74 " pdb=" CA THR G 74 " pdb=" C THR G 74 " ideal model delta sigma weight residual 111.28 106.41 4.87 1.09e+00 8.42e-01 2.00e+01 angle pdb=" N GLU B 76 " pdb=" CA GLU B 76 " pdb=" C GLU B 76 " ideal model delta sigma weight residual 110.43 115.76 -5.33 1.31e+00 5.83e-01 1.66e+01 angle pdb=" C ILE F 266 " pdb=" CA ILE F 266 " pdb=" CB ILE F 266 " ideal model delta sigma weight residual 113.70 109.87 3.83 9.50e-01 1.11e+00 1.63e+01 angle pdb=" N TRP B 174 " pdb=" CA TRP B 174 " pdb=" C TRP B 174 " ideal model delta sigma weight residual 111.36 115.66 -4.30 1.09e+00 8.42e-01 1.56e+01 ... (remaining 21016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 8217 17.83 - 35.65: 741 35.65 - 53.48: 179 53.48 - 71.31: 46 71.31 - 89.14: 20 Dihedral angle restraints: 9203 sinusoidal: 4035 harmonic: 5168 Sorted by residual: dihedral pdb=" CA TYR B 110 " pdb=" C TYR B 110 " pdb=" N TYR B 111 " pdb=" CA TYR B 111 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLN F 168 " pdb=" C GLN F 168 " pdb=" N ARG F 169 " pdb=" CA ARG F 169 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA TYR G 110 " pdb=" C TYR G 110 " pdb=" N TYR G 111 " pdb=" CA TYR G 111 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 9200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1758 0.045 - 0.090: 291 0.090 - 0.135: 121 0.135 - 0.180: 11 0.180 - 0.225: 2 Chirality restraints: 2183 Sorted by residual: chirality pdb=" CA PHE A 206 " pdb=" N PHE A 206 " pdb=" C PHE A 206 " pdb=" CB PHE A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C3' A K 3 " pdb=" C4' A K 3 " pdb=" O3' A K 3 " pdb=" C2' A K 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA VAL G 85 " pdb=" N VAL G 85 " pdb=" C VAL G 85 " pdb=" CB VAL G 85 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 2180 not shown) Planarity restraints: 2639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 76 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C GLU B 76 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU B 76 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG B 77 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 103 " 0.012 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ALA G 103 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA G 103 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP G 104 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 79 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C TRP B 79 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP B 79 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 80 " -0.013 2.00e-02 2.50e+03 ... (remaining 2636 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3437 2.79 - 3.32: 14109 3.32 - 3.85: 23897 3.85 - 4.37: 28511 4.37 - 4.90: 48814 Nonbonded interactions: 118768 Sorted by model distance: nonbonded pdb=" OH TYR E 79 " pdb=" O PRO E 91 " model vdw 2.264 3.040 nonbonded pdb=" OE2 GLU F 191 " pdb=" OH TYR F 222 " model vdw 2.271 3.040 nonbonded pdb=" N GLU E 64 " pdb=" OE1 GLU E 64 " model vdw 2.272 3.120 nonbonded pdb=" OG1 THR I 23 " pdb=" O LYS I 55 " model vdw 2.301 3.040 nonbonded pdb=" OE1 GLN F 57 " pdb=" OH TYR F 59 " model vdw 2.305 3.040 ... (remaining 118763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = (chain 'H' and resid 7 through 156) } ncs_group { reference = (chain 'D' and (resid 2 through 80 or resid 89 through 96)) selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 38.650 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15510 Z= 0.205 Angle : 0.575 6.657 21025 Z= 0.334 Chirality : 0.041 0.225 2183 Planarity : 0.005 0.065 2639 Dihedral : 15.035 89.136 5851 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.01 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (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 TRP 0.015 0.001 TRP C 113 HIS 0.008 0.001 HIS J 27 PHE 0.013 0.001 PHE A 206 TYR 0.017 0.001 TYR J 79 ARG 0.010 0.000 ARG B 41 Details of bonding type rmsd hydrogen bonds : bond 0.14364 ( 662) hydrogen bonds : angle 6.04121 ( 1902) metal coordination : bond 0.00417 ( 20) metal coordination : angle 3.53846 ( 4) covalent geometry : bond 0.00357 (15490) covalent geometry : angle 0.57328 (21021) *********************** 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 : 1.807 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: 0.4213 (mmt) cc_final: 0.3863 (mmp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.3358 time to fit residues: 128.4689 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 : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 0.1980 chunk 133 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 154 optimal weight: 20.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 35 HIS E 61 ASN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS G 105 GLN H 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.100608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.072091 restraints weight = 58365.701| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 4.60 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2021 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= 0.154 Angle : 0.618 6.944 21025 Z= 0.321 Chirality : 0.043 0.173 2183 Planarity : 0.005 0.063 2639 Dihedral : 7.901 60.052 2198 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.07 % Allowed : 8.22 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.20), residues: 1728 helix: 1.76 (0.22), residues: 616 sheet: -0.09 (0.27), residues: 360 loop : -0.02 (0.23), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 110 HIS 0.004 0.001 HIS B 108 PHE 0.020 0.002 PHE C 32 TYR 0.018 0.001 TYR E 79 ARG 0.006 0.001 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 662) hydrogen bonds : angle 5.15298 ( 1902) metal coordination : bond 0.00727 ( 20) metal coordination : angle 3.51097 ( 4) covalent geometry : bond 0.00343 (15490) covalent geometry : angle 0.61646 (21021) *********************** 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 209 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 192 time to evaluate : 1.897 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 152 MET cc_start: 0.8702 (mtm) cc_final: 0.8462 (mtm) REVERT: E 70 LEU cc_start: 0.9013 (tt) cc_final: 0.8695 (tp) REVERT: E 74 CYS cc_start: 0.7974 (m) cc_final: 0.7483 (m) REVERT: F 219 TYR cc_start: 0.7531 (m-80) cc_final: 0.7086 (m-10) REVERT: F 259 GLU cc_start: 0.7746 (mp0) cc_final: 0.7514 (pm20) REVERT: F 285 TRP cc_start: 0.6837 (m100) cc_final: 0.6604 (m100) REVERT: G 1 MET cc_start: 0.7575 (ppp) cc_final: 0.7158 (ppp) REVERT: G 54 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8351 (tt0) REVERT: G 101 GLU cc_start: 0.9032 (mp0) cc_final: 0.8792 (mp0) REVERT: G 168 LYS cc_start: 0.9103 (tmtt) cc_final: 0.8660 (tptp) REVERT: H 64 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6348 (tp) REVERT: J 105 MET cc_start: 0.4573 (mmt) cc_final: 0.4339 (mmp) outliers start: 17 outliers final: 9 residues processed: 198 average time/residue: 0.3396 time to fit residues: 99.3971 Evaluate side-chains 168 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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 E residue 63 ARG Chi-restraints excluded: chain G residue 23 SER 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 137 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 134 optimal weight: 30.0000 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.097984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.067451 restraints weight = 58150.134| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.98 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15510 Z= 0.234 Angle : 0.625 10.359 21025 Z= 0.322 Chirality : 0.043 0.188 2183 Planarity : 0.005 0.059 2639 Dihedral : 7.882 59.686 2198 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.90 % Allowed : 10.68 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1728 helix: 1.75 (0.22), residues: 614 sheet: -0.48 (0.26), residues: 365 loop : 0.03 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 361 HIS 0.007 0.001 HIS B 73 PHE 0.040 0.002 PHE E 77 TYR 0.014 0.002 TYR E 79 ARG 0.009 0.001 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.03856 ( 662) hydrogen bonds : angle 5.06012 ( 1902) metal coordination : bond 0.01004 ( 20) metal coordination : angle 5.03787 ( 4) covalent geometry : bond 0.00524 (15490) covalent geometry : angle 0.62112 (21021) *********************** 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 200 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 1.813 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 338 MET cc_start: 0.9134 (mmm) cc_final: 0.8732 (mmm) REVERT: D 80 ARG cc_start: 0.6891 (ttp-170) cc_final: 0.6606 (mmp-170) REVERT: E 70 LEU cc_start: 0.9129 (tt) cc_final: 0.8804 (tt) REVERT: E 74 CYS cc_start: 0.7670 (m) cc_final: 0.7300 (m) REVERT: E 104 LEU cc_start: 0.9055 (tp) cc_final: 0.8782 (mt) REVERT: F 219 TYR cc_start: 0.7620 (m-80) cc_final: 0.7202 (m-10) REVERT: F 259 GLU cc_start: 0.7826 (mp0) cc_final: 0.7555 (pm20) REVERT: F 285 TRP cc_start: 0.7034 (m100) cc_final: 0.6807 (m100) REVERT: G 1 MET cc_start: 0.7267 (ppp) cc_final: 0.6762 (ppp) REVERT: G 54 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8280 (tt0) REVERT: G 101 GLU cc_start: 0.9026 (mp0) cc_final: 0.8765 (mp0) REVERT: G 168 LYS cc_start: 0.9125 (tmtt) cc_final: 0.8680 (tptp) outliers start: 30 outliers final: 18 residues processed: 184 average time/residue: 0.3039 time to fit residues: 85.1963 Evaluate side-chains 171 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 1.769 ------------------------------------------------------------------------------- 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 D residue 12 THR Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 90 ILE 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 55 VAL Chi-restraints excluded: chain G residue 74 THR 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 106 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 138 optimal weight: 0.1980 chunk 69 optimal weight: 20.0000 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 HIS ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.099407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.069087 restraints weight = 57865.916| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 4.93 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2795 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= 0.119 Angle : 0.567 8.357 21025 Z= 0.290 Chirality : 0.041 0.176 2183 Planarity : 0.004 0.065 2639 Dihedral : 7.618 59.467 2198 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.71 % Allowed : 12.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1728 helix: 1.77 (0.22), residues: 622 sheet: -0.22 (0.26), residues: 374 loop : 0.10 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 211 HIS 0.008 0.001 HIS B 80 PHE 0.015 0.001 PHE D 15 TYR 0.019 0.001 TYR B 147 ARG 0.007 0.000 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.03184 ( 662) hydrogen bonds : angle 4.77561 ( 1902) metal coordination : bond 0.00499 ( 20) metal coordination : angle 3.68105 ( 4) covalent geometry : bond 0.00268 (15490) covalent geometry : angle 0.56513 (21021) *********************** 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: 27 poor density : 172 time to evaluate : 1.813 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: 0.8065 (mmm160) cc_final: 0.7664 (mmp80) REVERT: A 152 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8482 (mtm) REVERT: A 268 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7612 (t80) REVERT: A 338 MET cc_start: 0.9055 (mmm) cc_final: 0.8809 (mmm) REVERT: E 70 LEU cc_start: 0.9226 (tt) cc_final: 0.8931 (tp) REVERT: E 74 CYS cc_start: 0.7455 (m) cc_final: 0.7142 (m) REVERT: E 104 LEU cc_start: 0.9050 (tp) cc_final: 0.8767 (mt) REVERT: F 219 TYR cc_start: 0.7502 (m-80) cc_final: 0.7203 (m-10) REVERT: F 259 GLU cc_start: 0.7876 (mp0) cc_final: 0.7565 (pm20) REVERT: F 272 ASP cc_start: 0.7486 (t0) cc_final: 0.7277 (t70) REVERT: F 285 TRP cc_start: 0.6903 (m100) cc_final: 0.6696 (m100) REVERT: G 1 MET cc_start: 0.7364 (ppp) cc_final: 0.6772 (ppp) REVERT: G 34 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.8013 (mmmm) REVERT: G 101 GLU cc_start: 0.8990 (mp0) cc_final: 0.8782 (mp0) REVERT: G 168 LYS cc_start: 0.9118 (tmtt) cc_final: 0.8681 (tptp) REVERT: H 64 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6677 (tp) outliers start: 27 outliers final: 18 residues processed: 188 average time/residue: 0.2783 time to fit residues: 77.8448 Evaluate side-chains 182 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET 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 E residue 60 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR 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 34 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.098220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067947 restraints weight = 58537.627| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 4.67 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15510 Z= 0.162 Angle : 0.575 14.379 21025 Z= 0.293 Chirality : 0.041 0.200 2183 Planarity : 0.004 0.051 2639 Dihedral : 7.598 59.413 2198 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.34 % Allowed : 12.83 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1728 helix: 1.67 (0.21), residues: 630 sheet: -0.37 (0.26), residues: 364 loop : 0.03 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP F 361 HIS 0.006 0.001 HIS G 48 PHE 0.048 0.001 PHE E 77 TYR 0.016 0.001 TYR B 147 ARG 0.007 0.000 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.03342 ( 662) hydrogen bonds : angle 4.72528 ( 1902) metal coordination : bond 0.00716 ( 20) metal coordination : angle 3.68132 ( 4) covalent geometry : bond 0.00366 (15490) covalent geometry : angle 0.57271 (21021) *********************** 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 202 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 1.726 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: A 152 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8506 (mtm) REVERT: A 227 MET cc_start: 0.7970 (mmm) cc_final: 0.7219 (mmm) REVERT: A 268 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7723 (t80) REVERT: B 14 ASP cc_start: 0.8871 (p0) cc_final: 0.8357 (p0) REVERT: D 45 TYR cc_start: 0.7218 (m-80) cc_final: 0.6898 (m-80) REVERT: D 48 ASP cc_start: 0.6578 (t0) cc_final: 0.5738 (t0) REVERT: E 104 LEU cc_start: 0.9099 (tp) cc_final: 0.8785 (mt) REVERT: F 219 TYR cc_start: 0.7581 (m-80) cc_final: 0.7312 (m-10) REVERT: F 259 GLU cc_start: 0.7886 (mp0) cc_final: 0.7528 (pm20) REVERT: F 272 ASP cc_start: 0.7521 (t0) cc_final: 0.7315 (t70) REVERT: G 1 MET cc_start: 0.7372 (ppp) cc_final: 0.6781 (ppp) REVERT: G 34 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7934 (mmmm) REVERT: G 101 GLU cc_start: 0.9018 (mp0) cc_final: 0.8797 (mp0) REVERT: G 168 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8723 (tptp) REVERT: H 28 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7546 (mppt) REVERT: H 98 LYS cc_start: 0.9145 (tttt) cc_final: 0.8878 (ttmt) REVERT: H 122 MET cc_start: 0.8057 (mmm) cc_final: 0.7659 (mmm) outliers start: 37 outliers final: 23 residues processed: 189 average time/residue: 0.2742 time to fit residues: 78.3440 Evaluate side-chains 180 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET 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 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 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 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 Chi-restraints excluded: chain I residue 16 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 0.1980 chunk 65 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 0.0170 chunk 150 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN G 28 HIS ** J 108 ASN ** 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 = 0.4098 r_free = 0.4098 target = 0.098810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.068661 restraints weight = 58415.262| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 4.71 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15510 Z= 0.121 Angle : 0.563 10.076 21025 Z= 0.286 Chirality : 0.040 0.175 2183 Planarity : 0.004 0.051 2639 Dihedral : 7.516 59.293 2198 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.21 % Allowed : 13.27 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1728 helix: 1.69 (0.21), residues: 632 sheet: -0.31 (0.26), residues: 363 loop : 0.05 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 361 HIS 0.009 0.001 HIS G 48 PHE 0.015 0.001 PHE E 77 TYR 0.018 0.001 TYR B 147 ARG 0.011 0.000 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 662) hydrogen bonds : angle 4.62672 ( 1902) metal coordination : bond 0.00467 ( 20) metal coordination : angle 2.96771 ( 4) covalent geometry : bond 0.00278 (15490) covalent geometry : angle 0.56172 (21021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.839 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 152 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8464 (mtm) REVERT: A 227 MET cc_start: 0.8055 (mmm) cc_final: 0.7098 (mmm) REVERT: A 268 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7649 (t80) REVERT: B 14 ASP cc_start: 0.8764 (p0) cc_final: 0.8268 (p0) REVERT: B 70 TRP cc_start: 0.7872 (OUTLIER) cc_final: 0.7527 (m-10) REVERT: B 78 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7633 (t0) REVERT: D 45 TYR cc_start: 0.7287 (m-80) cc_final: 0.6924 (m-80) REVERT: D 48 ASP cc_start: 0.6587 (t0) cc_final: 0.5763 (t0) REVERT: E 104 LEU cc_start: 0.9075 (tp) cc_final: 0.8747 (mt) REVERT: F 219 TYR cc_start: 0.7557 (m-80) cc_final: 0.7263 (m-10) REVERT: F 259 GLU cc_start: 0.7914 (mp0) cc_final: 0.7570 (pm20) REVERT: F 272 ASP cc_start: 0.7536 (t0) cc_final: 0.7318 (t70) REVERT: G 1 MET cc_start: 0.7463 (ppp) cc_final: 0.6821 (ppp) REVERT: G 99 ASP cc_start: 0.8348 (t0) cc_final: 0.8145 (t0) REVERT: G 168 LYS cc_start: 0.9110 (tmtt) cc_final: 0.8682 (tptp) REVERT: H 28 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7506 (mppt) REVERT: H 122 MET cc_start: 0.7984 (mmm) cc_final: 0.7127 (mmm) outliers start: 35 outliers final: 22 residues processed: 185 average time/residue: 0.2848 time to fit residues: 79.7001 Evaluate side-chains 181 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET 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 C residue 97 LEU 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 F residue 311 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 16 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 77 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 146 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 147 optimal weight: 0.0040 chunk 98 optimal weight: 0.7980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 GLN ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.099348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.069311 restraints weight = 58584.151| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 4.89 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15510 Z= 0.104 Angle : 0.554 14.095 21025 Z= 0.278 Chirality : 0.040 0.180 2183 Planarity : 0.004 0.050 2639 Dihedral : 7.448 59.233 2198 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.96 % Allowed : 13.78 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.21), residues: 1728 helix: 1.74 (0.21), residues: 632 sheet: -0.05 (0.26), residues: 387 loop : 0.10 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 211 HIS 0.006 0.001 HIS G 48 PHE 0.048 0.001 PHE E 77 TYR 0.012 0.001 TYR B 147 ARG 0.010 0.000 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.02924 ( 662) hydrogen bonds : angle 4.53721 ( 1902) metal coordination : bond 0.00485 ( 20) metal coordination : angle 3.09802 ( 4) covalent geometry : bond 0.00237 (15490) covalent geometry : angle 0.55267 (21021) *********************** 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 193 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 1.645 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 152 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8459 (mtm) REVERT: A 227 MET cc_start: 0.8100 (mmm) cc_final: 0.7255 (mmm) REVERT: A 268 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7615 (t80) REVERT: B 14 ASP cc_start: 0.8760 (p0) cc_final: 0.8316 (p0) REVERT: B 70 TRP cc_start: 0.7765 (OUTLIER) cc_final: 0.7481 (m-10) REVERT: B 78 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7882 (t70) REVERT: D 45 TYR cc_start: 0.7327 (m-80) cc_final: 0.6923 (m-80) REVERT: D 48 ASP cc_start: 0.6577 (t0) cc_final: 0.5749 (t0) REVERT: E 104 LEU cc_start: 0.9053 (tp) cc_final: 0.8717 (mt) REVERT: F 219 TYR cc_start: 0.7535 (m-80) cc_final: 0.7279 (m-10) REVERT: F 259 GLU cc_start: 0.7900 (mp0) cc_final: 0.7543 (pm20) REVERT: F 277 TYR cc_start: 0.7991 (m-80) cc_final: 0.7681 (m-80) REVERT: G 1 MET cc_start: 0.7720 (ppp) cc_final: 0.7108 (ppp) REVERT: G 168 LYS cc_start: 0.9131 (tmtt) cc_final: 0.8714 (tptp) REVERT: H 28 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7571 (mppt) REVERT: H 122 MET cc_start: 0.8067 (mmm) cc_final: 0.7249 (mmm) outliers start: 31 outliers final: 22 residues processed: 182 average time/residue: 0.2479 time to fit residues: 68.6139 Evaluate side-chains 178 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET 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 C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU 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 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 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 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 133 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.096746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.066462 restraints weight = 58995.994| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 4.77 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15510 Z= 0.253 Angle : 0.633 11.275 21025 Z= 0.324 Chirality : 0.043 0.251 2183 Planarity : 0.005 0.053 2639 Dihedral : 7.668 59.286 2198 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.21 % Allowed : 14.10 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.20), residues: 1728 helix: 1.63 (0.21), residues: 630 sheet: -0.39 (0.26), residues: 361 loop : -0.02 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 211 HIS 0.006 0.001 HIS F 257 PHE 0.035 0.002 PHE H 18 TYR 0.023 0.002 TYR B 147 ARG 0.008 0.001 ARG H 19 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 662) hydrogen bonds : angle 4.79824 ( 1902) metal coordination : bond 0.00929 ( 20) metal coordination : angle 4.34645 ( 4) covalent geometry : bond 0.00568 (15490) covalent geometry : angle 0.63015 (21021) *********************** 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 191 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 1.683 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: B 14 ASP cc_start: 0.8775 (p0) cc_final: 0.8335 (p0) REVERT: B 78 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7897 (t0) REVERT: D 45 TYR cc_start: 0.7413 (m-80) cc_final: 0.7020 (m-80) REVERT: D 48 ASP cc_start: 0.6629 (t0) cc_final: 0.5805 (t0) REVERT: E 104 LEU cc_start: 0.9123 (tp) cc_final: 0.8766 (mt) REVERT: F 259 GLU cc_start: 0.7902 (mp0) cc_final: 0.7664 (pm20) REVERT: G 1 MET cc_start: 0.7359 (ppp) cc_final: 0.6735 (ppp) REVERT: G 168 LYS cc_start: 0.9138 (tmtt) cc_final: 0.8705 (tptp) REVERT: H 28 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7629 (mppt) REVERT: H 122 MET cc_start: 0.8003 (mmm) cc_final: 0.7351 (mmm) outliers start: 35 outliers final: 25 residues processed: 179 average time/residue: 0.2828 time to fit residues: 75.4434 Evaluate side-chains 176 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 97 LEU 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 E residue 90 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN F 275 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.098444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.068297 restraints weight = 58215.651| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.82 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15510 Z= 0.119 Angle : 0.599 11.139 21025 Z= 0.303 Chirality : 0.041 0.163 2183 Planarity : 0.004 0.048 2639 Dihedral : 7.523 59.076 2198 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.71 % Allowed : 15.17 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.21), residues: 1728 helix: 1.67 (0.21), residues: 633 sheet: -0.16 (0.27), residues: 353 loop : 0.01 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP F 361 HIS 0.006 0.001 HIS G 48 PHE 0.053 0.001 PHE E 77 TYR 0.018 0.001 TYR B 147 ARG 0.006 0.000 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.03147 ( 662) hydrogen bonds : angle 4.70056 ( 1902) metal coordination : bond 0.00435 ( 20) metal coordination : angle 2.95103 ( 4) covalent geometry : bond 0.00272 (15490) covalent geometry : angle 0.59816 (21021) *********************** 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 191 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.7643 (mmm) cc_final: 0.7094 (mmm) REVERT: A 268 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7737 (t80) REVERT: B 14 ASP cc_start: 0.8750 (p0) cc_final: 0.8344 (p0) REVERT: B 70 TRP cc_start: 0.7853 (OUTLIER) cc_final: 0.7470 (m-10) REVERT: D 45 TYR cc_start: 0.7360 (m-80) cc_final: 0.6961 (m-80) REVERT: D 48 ASP cc_start: 0.6638 (t0) cc_final: 0.5808 (t0) REVERT: F 259 GLU cc_start: 0.7916 (mp0) cc_final: 0.7683 (pm20) REVERT: F 277 TYR cc_start: 0.8012 (m-80) cc_final: 0.7729 (m-80) REVERT: F 338 MET cc_start: 0.5910 (mpp) cc_final: 0.4615 (mpp) REVERT: G 1 MET cc_start: 0.7372 (ppp) cc_final: 0.6741 (ppp) REVERT: G 168 LYS cc_start: 0.9133 (tmtt) cc_final: 0.8718 (tptp) REVERT: H 28 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7614 (mppt) REVERT: H 122 MET cc_start: 0.7960 (mmm) cc_final: 0.7265 (mmm) outliers start: 27 outliers final: 22 residues processed: 182 average time/residue: 0.2698 time to fit residues: 73.7045 Evaluate side-chains 179 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 80 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU 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 F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 17 PHE 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 41 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 168 optimal weight: 7.9990 chunk 169 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 0.0770 chunk 166 optimal weight: 5.9990 chunk 135 optimal weight: 0.0980 chunk 133 optimal weight: 4.9990 overall best weight: 1.2344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.098452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.068533 restraints weight = 59154.789| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 4.81 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15510 Z= 0.129 Angle : 0.603 14.422 21025 Z= 0.303 Chirality : 0.041 0.168 2183 Planarity : 0.004 0.048 2639 Dihedral : 7.500 59.102 2198 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.64 % Allowed : 15.23 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1728 helix: 1.63 (0.21), residues: 633 sheet: -0.17 (0.27), residues: 355 loop : 0.04 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 361 HIS 0.005 0.001 HIS G 48 PHE 0.031 0.001 PHE J 77 TYR 0.016 0.001 TYR B 147 ARG 0.004 0.000 ARG D 68 Details of bonding type rmsd hydrogen bonds : bond 0.03158 ( 662) hydrogen bonds : angle 4.70844 ( 1902) metal coordination : bond 0.00505 ( 20) metal coordination : angle 2.83904 ( 4) covalent geometry : bond 0.00295 (15490) covalent geometry : angle 0.60222 (21021) ********************** 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 186 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.665 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: A 227 MET cc_start: 0.7828 (mmm) cc_final: 0.7271 (mmm) REVERT: A 268 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7747 (t80) REVERT: B 14 ASP cc_start: 0.8802 (p0) cc_final: 0.8401 (p0) REVERT: D 45 TYR cc_start: 0.7549 (m-80) cc_final: 0.7067 (m-80) REVERT: D 48 ASP cc_start: 0.6832 (t0) cc_final: 0.6050 (t0) REVERT: E 104 LEU cc_start: 0.8990 (tp) cc_final: 0.8670 (mt) REVERT: F 259 GLU cc_start: 0.7938 (mp0) cc_final: 0.7702 (pm20) REVERT: F 277 TYR cc_start: 0.8022 (m-80) cc_final: 0.7710 (m-80) REVERT: F 338 MET cc_start: 0.5655 (mpp) cc_final: 0.4405 (mpp) REVERT: G 1 MET cc_start: 0.7331 (ppp) cc_final: 0.6650 (ppp) REVERT: G 39 PHE cc_start: 0.8555 (m-80) cc_final: 0.8349 (m-80) REVERT: G 168 LYS cc_start: 0.9147 (tmtt) cc_final: 0.8737 (tptp) REVERT: H 28 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7662 (mppt) REVERT: H 122 MET cc_start: 0.7946 (mmm) cc_final: 0.7296 (mmm) outliers start: 26 outliers final: 24 residues processed: 178 average time/residue: 0.2559 time to fit residues: 69.1671 Evaluate side-chains 183 residues out of total 1582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 1.837 ------------------------------------------------------------------------------- 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 80 HIS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU 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 F residue 140 GLN Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 17 PHE 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 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 50 optimal weight: 0.0980 chunk 100 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.099218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.069356 restraints weight = 59014.367| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 4.97 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15510 Z= 0.106 Angle : 0.600 14.625 21025 Z= 0.301 Chirality : 0.041 0.147 2183 Planarity : 0.004 0.046 2639 Dihedral : 7.446 59.033 2198 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.90 % Allowed : 15.17 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.21), residues: 1728 helix: 1.65 (0.21), residues: 633 sheet: -0.15 (0.27), residues: 361 loop : 0.12 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP F 361 HIS 0.005 0.001 HIS G 48 PHE 0.062 0.001 PHE E 77 TYR 0.022 0.001 TYR B 147 ARG 0.005 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.02993 ( 662) hydrogen bonds : angle 4.64659 ( 1902) metal coordination : bond 0.00350 ( 20) metal coordination : angle 2.42768 ( 4) covalent geometry : bond 0.00240 (15490) covalent geometry : angle 0.59871 (21021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8547.87 seconds wall clock time: 147 minutes 28.68 seconds (8848.68 seconds total)