Starting phenix.real_space_refine on Fri Jul 3 17:15:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cx1_27033/07_2026/8cx1_27033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cx1_27033/07_2026/8cx1_27033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cx1_27033/07_2026/8cx1_27033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cx1_27033/07_2026/8cx1_27033.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8cx1_27033/07_2026/8cx1_27033.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cx1_27033/07_2026/8cx1_27033.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cx1_27033/07_2026/8cx1_27033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cx1_27033/07_2026/8cx1_27033.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 16 5.49 5 S 96 5.16 5 C 9618 2.51 5 N 2686 2.21 5 O 2762 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15184 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3247 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 20, 'TRANS': 360} 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: 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: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 1 Chain: "F" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3228 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 19, 'TRANS': 358} Chain breaks: 1 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: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1261 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 4, 'TRANS': 146} 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: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 761 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain breaks: 1 Chain: "K" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 3} Chain: "L" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 3} 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 2502 SG CYS A 288 42.030 21.534 43.933 1.00 47.72 S ATOM 2525 SG CYS A 291 42.651 24.950 44.112 1.00 37.27 S ATOM 869 SG CYS A 97 59.400 59.302 51.544 1.00 18.43 S ATOM 891 SG CYS A 100 62.215 59.354 53.235 1.00 18.86 S ATOM 4231 SG CYS B 114 32.654 86.941 53.193 1.00 36.79 S ATOM 4375 SG CYS B 133 36.263 86.031 54.456 1.00 38.93 S ATOM 9915 SG CYS F 288 37.805 24.096 99.023 1.00 69.54 S ATOM 9938 SG CYS F 291 38.741 27.149 98.924 1.00 57.72 S ATOM 8301 SG CYS F 97 38.650 65.124 88.704 1.00 32.31 S ATOM 8323 SG CYS F 100 36.226 66.030 87.464 1.00 34.28 S ATOM 11644 SG CYS G 114 74.484 78.383 86.004 1.00 74.52 S ATOM 11788 SG CYS G 133 70.979 78.633 84.619 1.00 73.68 S Time building chain proxies: 2.98, per 1000 atoms: 0.20 Number of scatterers: 15184 At special positions: 0 Unit cell: (103.54, 144.455, 141.115, 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 96 16.00 P 16 15.00 O 2762 8.00 N 2686 7.00 C 9618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.05 Conformation dependent library (CDL) restraints added in 574.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 257 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 291 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 288 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 65 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 97 " 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 133 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 114 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 288 " pdb="ZN ZN F 501 " - pdb=" ND1 HIS F 257 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 291 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 100 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 97 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 65 " 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 133 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 114 " Number of angles added : 4 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3392 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 12 sheets defined 39.1% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 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: 3.665A pdb=" N LYS A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' 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 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 319 through 332 Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.630A 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: 3.737A pdb=" N SER B 46 " --> pdb=" O HIS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.867A 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 14 Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 71 through 75 removed outlier: 3.789A pdb=" N GLY C 75 " --> pdb=" O ALA C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 75' Processing helix chain 'C' and resid 129 through 135 removed outlier: 3.618A pdb=" N GLN C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 149 removed outlier: 3.578A pdb=" N GLN C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.781A pdb=" N GLY D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 4.448A 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 32 through 38 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: 4.237A pdb=" N LEU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 22 removed outlier: 3.589A 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 79 removed outlier: 3.622A pdb=" N LYS F 76 " --> pdb=" O HIS F 72 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS F 79 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 111 Processing helix chain 'F' and resid 128 through 139 Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 177 through 194 Processing helix chain 'F' and resid 198 through 206 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 319 through 332 removed outlier: 3.823A pdb=" N GLU F 323 " --> pdb=" O GLY F 319 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 350 Processing helix chain 'F' and resid 363 through 381 removed outlier: 3.993A pdb=" N ALA F 377 " --> pdb=" O GLY F 373 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU F 379 " --> pdb=" O LEU F 375 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLN F 380 " --> pdb=" O ARG F 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 31 Processing helix chain 'G' and resid 99 through 108 Processing helix chain 'G' and resid 118 through 126 removed outlier: 3.920A pdb=" N LYS G 122 " --> pdb=" O SER G 118 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA G 123 " --> pdb=" O ALA G 119 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU G 124 " --> pdb=" O ILE G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 removed outlier: 3.652A pdb=" N GLY G 138 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS G 139 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN G 140 " --> pdb=" O ALA G 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 135 through 140' Processing helix chain 'G' and resid 144 through 154 Processing helix chain 'G' and resid 165 through 170 Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 36 through 51 Processing helix chain 'H' and resid 129 through 135 removed outlier: 4.453A pdb=" N GLN H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 149 removed outlier: 4.176A pdb=" N GLN H 140 " --> pdb=" O ASP H 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 36 removed outlier: 3.707A pdb=" N GLY I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 4.374A 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 37 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: 4.101A pdb=" N LEU J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.538A 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 57 removed outlier: 3.508A pdb=" N ASP A 50 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP A 34 " --> pdb=" O SER A 93 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TRP A 94 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR A 148 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 116 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LYS A 150 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.295A 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: 9.440A pdb=" N LEU A 234 " --> pdb=" O HIS A 228 " (cutoff:3.500A) removed outlier: 10.582A pdb=" N HIS A 228 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N ASN A 236 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 11.183A pdb=" N ARG A 226 " --> pdb=" O ASN A 236 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ARG A 238 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N LYS A 334 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU A 307 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N SER A 336 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 309 " --> pdb=" O SER A 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.999A pdb=" N ASP C 120 " --> pdb=" O ASP C 115 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP C 115 " --> pdb=" O ASP C 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.760A pdb=" N GLN B 83 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.382A 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 removed outlier: 3.760A pdb=" N GLN B 83 " --> pdb=" O VAL B 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 12 through 18 removed outlier: 4.404A pdb=" N ALA D 73 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 6 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL D 75 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU D 77 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.303A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 8 through 9 removed outlier: 3.502A pdb=" N VAL F 9 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE F 53 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP F 50 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 231 through 243 removed outlier: 5.044A pdb=" N VAL F 224 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 9.407A pdb=" N GLN F 237 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 9.797A pdb=" N TYR F 222 " --> pdb=" O GLN F 237 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N ARG F 239 " --> pdb=" O LEU F 220 " (cutoff:3.500A) removed outlier: 11.826A pdb=" N LEU F 220 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS F 334 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41 removed outlier: 4.318A pdb=" N SER G 53 " --> pdb=" O THR G 68 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 64 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY G 84 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN G 83 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 13 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ILE G 87 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE G 9 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 11.055A pdb=" N TRP G 89 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 14.210A pdb=" N VAL G 7 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE H 69 " --> pdb=" O GLN G 6 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET G 8 " --> pdb=" O GLN H 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN H 67 " --> pdb=" O MET G 8 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LEU H 64 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 55 " --> pdb=" O PHE H 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 16 through 18 removed outlier: 3.868A pdb=" N THR I 16 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA I 73 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL I 75 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 77 " --> pdb=" O ARG I 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 28 through 32 645 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2397 1.31 - 1.43: 4688 1.43 - 1.56: 8378 1.56 - 1.69: 30 1.69 - 1.81: 140 Bond restraints: 15633 Sorted by residual: bond pdb=" CA ARG G 19 " pdb=" C ARG G 19 " ideal model delta sigma weight residual 1.524 1.463 0.061 1.26e-02 6.30e+03 2.35e+01 bond pdb=" CA TYR B 69 " pdb=" C TYR B 69 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.23e-02 6.61e+03 2.18e+01 bond pdb=" CA GLN B 83 " pdb=" C GLN B 83 " ideal model delta sigma weight residual 1.526 1.463 0.063 1.37e-02 5.33e+03 2.13e+01 bond pdb=" CA LYS G 22 " pdb=" C LYS G 22 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.27e-02 6.20e+03 1.99e+01 bond pdb=" CA ASP G 104 " pdb=" C ASP G 104 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.29e-02 6.01e+03 1.68e+01 ... (remaining 15628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 20817 2.07 - 4.13: 327 4.13 - 6.20: 39 6.20 - 8.26: 12 8.26 - 10.33: 2 Bond angle restraints: 21197 Sorted by residual: angle pdb=" N ARG B 173 " pdb=" CA ARG B 173 " pdb=" C ARG B 173 " ideal model delta sigma weight residual 111.36 121.69 -10.33 1.09e+00 8.42e-01 8.98e+01 angle pdb=" N ILE B 18 " pdb=" CA ILE B 18 " pdb=" C ILE B 18 " ideal model delta sigma weight residual 110.42 118.09 -7.67 9.60e-01 1.09e+00 6.38e+01 angle pdb=" N ASP C 34 " pdb=" CA ASP C 34 " pdb=" C ASP C 34 " ideal model delta sigma weight residual 111.28 118.51 -7.23 1.09e+00 8.42e-01 4.40e+01 angle pdb=" N ASP H 34 " pdb=" CA ASP H 34 " pdb=" C ASP H 34 " ideal model delta sigma weight residual 111.75 119.48 -7.73 1.28e+00 6.10e-01 3.64e+01 angle pdb=" N ASN B 175 " pdb=" CA ASN B 175 " pdb=" C ASN B 175 " ideal model delta sigma weight residual 113.17 105.82 7.35 1.26e+00 6.30e-01 3.40e+01 ... (remaining 21192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 8260 17.52 - 35.04: 794 35.04 - 52.56: 163 52.56 - 70.07: 36 70.07 - 87.59: 16 Dihedral angle restraints: 9269 sinusoidal: 4036 harmonic: 5233 Sorted by residual: dihedral pdb=" CA GLU H 16 " pdb=" C GLU H 16 " pdb=" N PHE H 17 " pdb=" CA PHE H 17 " ideal model delta harmonic sigma weight residual 180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE C 17 " pdb=" C PHE C 17 " pdb=" N PHE C 18 " pdb=" CA PHE C 18 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU C 16 " pdb=" C GLU C 16 " pdb=" N PHE C 17 " pdb=" CA PHE C 17 " ideal model delta harmonic sigma weight residual 180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 9266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1968 0.072 - 0.143: 212 0.143 - 0.215: 7 0.215 - 0.287: 2 0.287 - 0.358: 1 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA ARG B 173 " pdb=" N ARG B 173 " pdb=" C ARG B 173 " pdb=" CB ARG B 173 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA PRO F 129 " pdb=" N PRO F 129 " pdb=" C PRO F 129 " pdb=" CB PRO F 129 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.20 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2187 not shown) Planarity restraints: 2675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 82 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLY G 82 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY G 82 " -0.026 2.00e-02 2.50e+03 pdb=" N GLN G 83 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 257 " 0.007 2.00e-02 2.50e+03 3.00e-02 1.35e+01 pdb=" CG HIS A 257 " 0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 257 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 HIS A 257 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS A 257 " 0.041 2.00e-02 2.50e+03 pdb=" NE2 HIS A 257 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 65 " 0.011 2.00e-02 2.50e+03 2.84e-02 1.21e+01 pdb=" CG HIS A 65 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS A 65 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 HIS A 65 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS A 65 " 0.041 2.00e-02 2.50e+03 pdb=" NE2 HIS A 65 " -0.008 2.00e-02 2.50e+03 ... (remaining 2672 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2914 2.78 - 3.31: 14567 3.31 - 3.84: 24469 3.84 - 4.37: 29376 4.37 - 4.90: 50293 Nonbonded interactions: 121619 Sorted by model distance: nonbonded pdb=" OG1 THR F 339 " pdb=" OE1 GLU F 342 " model vdw 2.244 3.040 nonbonded pdb=" N GLU E 56 " pdb=" OE1 GLU E 56 " model vdw 2.257 3.120 nonbonded pdb=" OG SER J 39 " pdb=" O LEU J 110 " model vdw 2.301 3.040 nonbonded pdb=" N GLU J 64 " pdb=" OE1 GLU J 64 " model vdw 2.303 3.120 nonbonded pdb=" O ASN B 3 " pdb=" OD1 ASN B 3 " model vdw 2.320 3.040 ... (remaining 121614 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' and (resid 1 through 142 or resid 146 through 502)) 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' selection = chain 'I' } ncs_group { reference = (chain 'E' and resid 9 through 112) selection = chain 'J' } ncs_group { reference = (chain 'K' and resid 0 through 6) selection = (chain 'L' and resid 0 through 6) } 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: 3.240 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: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.070 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 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 0.082 15653 Z= 0.258 Angle : 0.654 10.328 21201 Z= 0.398 Chirality : 0.043 0.358 2190 Planarity : 0.004 0.063 2675 Dihedral : 14.563 87.593 5877 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.06 % Allowed : 0.81 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1751 helix: 1.18 (0.21), residues: 615 sheet: -0.23 (0.28), residues: 322 loop : -0.55 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 77 TYR 0.013 0.001 TYR G 111 PHE 0.015 0.001 PHE J 77 TRP 0.010 0.001 TRP B 5 HIS 0.046 0.002 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.26 (15633) covalent geometry : angle 0.64937 / 0.40 (21197) hydrogen bonds : bond 0.13438 / 9.11 ( 642) hydrogen bonds : angle 6.04382 / 4.16 ( 1845) metal coordination : bond 0.02901 / 1.78 ( 20) metal coordination : angle 5.54118 / 3.11 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.551 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 LEU cc_start: 0.7215 (mt) cc_final: 0.6920 (pt) REVERT: E 32 LYS cc_start: 0.7155 (ttpp) cc_final: 0.6827 (mptt) outliers start: 1 outliers final: 1 residues processed: 291 average time/residue: 0.1372 time to fit residues: 54.5625 Evaluate side-chains 161 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 114 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 0.0000 chunk 149 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 HIS B 27 HIS ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN F 216 HIS F 275 GLN G 12 GLN ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 175 ASN H 37 HIS ** J 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.082774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.058431 restraints weight = 63010.870| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 5.05 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15653 Z= 0.197 Angle : 0.667 8.937 21201 Z= 0.348 Chirality : 0.044 0.302 2190 Planarity : 0.005 0.048 2675 Dihedral : 6.857 67.331 2176 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.19 % Allowed : 9.44 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1751 helix: 1.26 (0.21), residues: 625 sheet: 0.03 (0.28), residues: 328 loop : -0.47 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 374 TYR 0.026 0.002 TYR H 85 PHE 0.019 0.002 PHE J 62 TRP 0.033 0.002 TRP F 211 HIS 0.008 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.20 (15633) covalent geometry : angle 0.66515 / 0.35 (21197) hydrogen bonds : bond 0.03938 / 2.61 ( 642) hydrogen bonds : angle 5.27749 / 3.65 ( 1845) metal coordination : bond 0.00876 / 0.50 ( 20) metal coordination : angle 3.47549 / 1.75 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 ASP cc_start: 0.7242 (p0) cc_final: 0.7003 (p0) REVERT: C 18 PHE cc_start: 0.6916 (t80) cc_final: 0.6446 (t80) REVERT: C 20 LYS cc_start: 0.7915 (tptt) cc_final: 0.7611 (tptt) REVERT: C 122 MET cc_start: 0.7278 (tpp) cc_final: 0.7000 (tpp) REVERT: D 62 PHE cc_start: 0.1852 (m-80) cc_final: 0.1639 (m-80) REVERT: E 32 LYS cc_start: 0.7453 (ttpp) cc_final: 0.7194 (mptt) REVERT: F 104 MET cc_start: 0.9171 (mtt) cc_final: 0.8893 (mtp) REVERT: G 16 MET cc_start: 0.8316 (mpp) cc_final: 0.8076 (mpp) REVERT: H 9 ARG cc_start: 0.9057 (ttt90) cc_final: 0.8842 (mtp85) REVERT: H 127 PHE cc_start: 0.6481 (t80) cc_final: 0.5728 (t80) outliers start: 19 outliers final: 11 residues processed: 197 average time/residue: 0.1081 time to fit residues: 31.3466 Evaluate side-chains 161 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain G residue 73 HIS Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 12 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 161 optimal weight: 0.0370 overall best weight: 2.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.083149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.058249 restraints weight = 63314.481| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 5.11 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15653 Z= 0.160 Angle : 0.598 7.608 21201 Z= 0.313 Chirality : 0.041 0.156 2190 Planarity : 0.004 0.045 2675 Dihedral : 6.788 67.974 2175 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.06 % Allowed : 12.19 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1751 helix: 1.49 (0.22), residues: 613 sheet: 0.13 (0.28), residues: 343 loop : -0.38 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 213 TYR 0.026 0.001 TYR E 18 PHE 0.030 0.001 PHE F 262 TRP 0.031 0.002 TRP F 211 HIS 0.007 0.001 HIS F 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (15633) covalent geometry : angle 0.59657 / 0.31 (21197) hydrogen bonds : bond 0.03511 / 2.36 ( 642) hydrogen bonds : angle 5.04823 / 3.50 ( 1845) metal coordination : bond 0.00629 / 0.41 ( 20) metal coordination : angle 2.77134 / 1.54 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 GLN cc_start: 0.8958 (mt0) cc_final: 0.8681 (mp10) REVERT: C 19 ARG cc_start: 0.7428 (tpm170) cc_final: 0.7178 (tpm170) REVERT: C 122 MET cc_start: 0.7436 (tpp) cc_final: 0.7121 (tpp) REVERT: E 20 LYS cc_start: 0.9011 (ttmm) cc_final: 0.8704 (tppp) REVERT: E 32 LYS cc_start: 0.7400 (ttpp) cc_final: 0.7191 (mptt) REVERT: G 70 TRP cc_start: 0.7132 (OUTLIER) cc_final: 0.6622 (m-10) REVERT: G 99 ASP cc_start: 0.8378 (t0) cc_final: 0.7920 (p0) REVERT: G 113 ASP cc_start: 0.7296 (p0) cc_final: 0.6863 (p0) REVERT: H 9 ARG cc_start: 0.9068 (ttt90) cc_final: 0.8755 (mtp-110) REVERT: H 127 PHE cc_start: 0.6400 (t80) cc_final: 0.5283 (t80) outliers start: 17 outliers final: 11 residues processed: 173 average time/residue: 0.1106 time to fit residues: 28.5674 Evaluate side-chains 147 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 36 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 162 optimal weight: 30.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** 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 = 0.4011 r_free = 0.4011 target = 0.082094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.057441 restraints weight = 62896.080| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 5.05 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15653 Z= 0.185 Angle : 0.598 8.079 21201 Z= 0.314 Chirality : 0.042 0.208 2190 Planarity : 0.004 0.051 2675 Dihedral : 6.875 67.550 2175 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.81 % Allowed : 12.06 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1751 helix: 1.46 (0.22), residues: 617 sheet: 0.10 (0.28), residues: 348 loop : -0.42 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 320 TYR 0.020 0.001 TYR G 111 PHE 0.014 0.002 PHE F 70 TRP 0.031 0.002 TRP F 211 HIS 0.006 0.001 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (15633) covalent geometry : angle 0.59645 / 0.31 (21197) hydrogen bonds : bond 0.03490 / 2.32 ( 642) hydrogen bonds : angle 5.01948 / 3.50 ( 1845) metal coordination : bond 0.00909 / 0.51 ( 20) metal coordination : angle 2.67137 / 1.39 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.547 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: C 18 PHE cc_start: 0.7000 (t80) cc_final: 0.6293 (t80) REVERT: C 19 ARG cc_start: 0.7650 (tpm170) cc_final: 0.7306 (tpm170) REVERT: C 20 LYS cc_start: 0.7928 (tptt) cc_final: 0.7658 (tptt) REVERT: C 122 MET cc_start: 0.7653 (tpp) cc_final: 0.7354 (tpp) REVERT: E 20 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8721 (tppp) REVERT: E 32 LYS cc_start: 0.7241 (ttpp) cc_final: 0.6984 (mptt) REVERT: G 70 TRP cc_start: 0.7207 (OUTLIER) cc_final: 0.6689 (m-10) REVERT: G 99 ASP cc_start: 0.8303 (t0) cc_final: 0.7929 (p0) REVERT: H 9 ARG cc_start: 0.9094 (ttt90) cc_final: 0.8878 (mtp-110) outliers start: 29 outliers final: 20 residues processed: 174 average time/residue: 0.1061 time to fit residues: 27.2266 Evaluate side-chains 160 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 69 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 165 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 172 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** 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 = 0.3970 r_free = 0.3970 target = 0.080182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.055005 restraints weight = 64849.543| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 5.20 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15653 Z= 0.277 Angle : 0.675 7.368 21201 Z= 0.356 Chirality : 0.044 0.186 2190 Planarity : 0.005 0.048 2675 Dihedral : 7.269 65.302 2175 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.56 % Allowed : 13.94 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1751 helix: 1.18 (0.21), residues: 612 sheet: -0.00 (0.28), residues: 344 loop : -0.44 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 93 TYR 0.028 0.002 TYR G 111 PHE 0.032 0.002 PHE H 127 TRP 0.033 0.002 TRP F 211 HIS 0.008 0.002 HIS B 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.28 (15633) covalent geometry : angle 0.67302 / 0.36 (21197) hydrogen bonds : bond 0.04060 / 2.71 ( 642) hydrogen bonds : angle 5.19406 / 3.61 ( 1845) metal coordination : bond 0.01289 / 0.78 ( 20) metal coordination : angle 3.65523 / 1.92 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.653 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: C 18 PHE cc_start: 0.7280 (t80) cc_final: 0.6437 (t80) REVERT: C 19 ARG cc_start: 0.7784 (tpm170) cc_final: 0.7489 (tpm170) REVERT: C 122 MET cc_start: 0.7687 (tpp) cc_final: 0.7437 (tpp) REVERT: E 20 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8132 (ttmm) REVERT: E 21 LEU cc_start: 0.9341 (mt) cc_final: 0.8679 (pp) REVERT: E 32 LYS cc_start: 0.7307 (ttpp) cc_final: 0.7047 (mptt) REVERT: G 8 MET cc_start: 0.7671 (mmm) cc_final: 0.7461 (mmm) REVERT: G 78 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6219 (t0) REVERT: H 9 ARG cc_start: 0.9063 (ttt90) cc_final: 0.8634 (ptp-170) outliers start: 41 outliers final: 29 residues processed: 172 average time/residue: 0.1119 time to fit residues: 28.7793 Evaluate side-chains 155 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 45 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 7 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 136 optimal weight: 8.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.081910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.057268 restraints weight = 64051.798| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 5.00 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15653 Z= 0.123 Angle : 0.579 9.381 21201 Z= 0.301 Chirality : 0.041 0.205 2190 Planarity : 0.004 0.043 2675 Dihedral : 7.016 70.140 2175 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.81 % Allowed : 15.62 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.20), residues: 1751 helix: 1.54 (0.22), residues: 616 sheet: 0.24 (0.28), residues: 339 loop : -0.34 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 9 TYR 0.034 0.001 TYR E 18 PHE 0.025 0.001 PHE F 262 TRP 0.035 0.002 TRP B 174 HIS 0.006 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (15633) covalent geometry : angle 0.57751 / 0.30 (21197) hydrogen bonds : bond 0.03230 / 2.14 ( 642) hydrogen bonds : angle 4.79425 / 3.32 ( 1845) metal coordination : bond 0.00501 / 0.34 ( 20) metal coordination : angle 2.98470 / 1.59 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7338 (tt0) REVERT: C 18 PHE cc_start: 0.7297 (t80) cc_final: 0.6287 (t80) REVERT: C 122 MET cc_start: 0.7704 (tpp) cc_final: 0.7435 (tpp) REVERT: E 20 LYS cc_start: 0.8693 (ttmm) cc_final: 0.8401 (mtpp) REVERT: F 92 ILE cc_start: 0.9068 (mp) cc_final: 0.8838 (pt) REVERT: H 9 ARG cc_start: 0.9109 (ttt90) cc_final: 0.8568 (ptp-170) REVERT: J 21 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9098 (pp) outliers start: 29 outliers final: 16 residues processed: 154 average time/residue: 0.1126 time to fit residues: 26.6403 Evaluate side-chains 145 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 163 optimal weight: 40.0000 chunk 9 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** 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 = 0.3992 r_free = 0.3992 target = 0.081109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.056280 restraints weight = 63951.828| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 5.07 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15653 Z= 0.167 Angle : 0.612 11.025 21201 Z= 0.315 Chirality : 0.042 0.199 2190 Planarity : 0.004 0.050 2675 Dihedral : 7.039 68.439 2175 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.62 % Allowed : 16.88 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1751 helix: 1.58 (0.22), residues: 612 sheet: 0.27 (0.28), residues: 338 loop : -0.31 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 37 TYR 0.033 0.001 TYR E 18 PHE 0.014 0.001 PHE F 70 TRP 0.033 0.002 TRP F 211 HIS 0.008 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (15633) covalent geometry : angle 0.60999 / 0.32 (21197) hydrogen bonds : bond 0.03419 / 2.26 ( 642) hydrogen bonds : angle 4.82017 / 3.35 ( 1845) metal coordination : bond 0.00790 / 0.54 ( 20) metal coordination : angle 3.43493 / 1.81 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7363 (tt0) REVERT: C 18 PHE cc_start: 0.7138 (t80) cc_final: 0.6033 (t80) REVERT: C 20 LYS cc_start: 0.7844 (tptt) cc_final: 0.7568 (tptt) REVERT: C 122 MET cc_start: 0.7692 (tpp) cc_final: 0.7469 (tpp) REVERT: E 20 LYS cc_start: 0.8691 (ttmm) cc_final: 0.8415 (ttmm) REVERT: E 21 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8659 (pp) REVERT: E 54 GLU cc_start: 0.5447 (tt0) cc_final: 0.5237 (tp30) REVERT: G 113 ASP cc_start: 0.7242 (p0) cc_final: 0.6782 (t0) REVERT: H 9 ARG cc_start: 0.9022 (ttt90) cc_final: 0.8487 (ptp-170) REVERT: H 122 MET cc_start: 0.8752 (tmm) cc_final: 0.8470 (tmm) outliers start: 26 outliers final: 22 residues processed: 152 average time/residue: 0.1121 time to fit residues: 25.9160 Evaluate side-chains 148 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 137 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 133 optimal weight: 7.9990 chunk 73 optimal weight: 0.0040 chunk 161 optimal weight: 40.0000 chunk 134 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 overall best weight: 2.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.080737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.056678 restraints weight = 64769.856| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 5.07 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15653 Z= 0.182 Angle : 0.628 10.065 21201 Z= 0.324 Chirality : 0.042 0.198 2190 Planarity : 0.004 0.045 2675 Dihedral : 7.080 68.524 2175 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.00 % Allowed : 16.75 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.20), residues: 1751 helix: 1.55 (0.22), residues: 613 sheet: 0.21 (0.28), residues: 342 loop : -0.28 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 213 TYR 0.041 0.001 TYR E 18 PHE 0.014 0.001 PHE F 70 TRP 0.032 0.002 TRP B 174 HIS 0.010 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (15633) covalent geometry : angle 0.62559 / 0.32 (21197) hydrogen bonds : bond 0.03456 / 2.28 ( 642) hydrogen bonds : angle 4.81183 / 3.34 ( 1845) metal coordination : bond 0.00852 / 0.57 ( 20) metal coordination : angle 3.76735 / 2.06 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.576 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: B 54 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7407 (tt0) REVERT: C 20 LYS cc_start: 0.7893 (tptt) cc_final: 0.7613 (tptt) REVERT: C 122 MET cc_start: 0.7740 (tpp) cc_final: 0.7538 (tpp) REVERT: F 152 MET cc_start: 0.7422 (mtm) cc_final: 0.6629 (mtm) REVERT: F 193 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8298 (tt) REVERT: F 366 GLU cc_start: 0.9344 (OUTLIER) cc_final: 0.9129 (pm20) REVERT: G 113 ASP cc_start: 0.7364 (p0) cc_final: 0.6917 (t0) REVERT: J 21 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9108 (tt) outliers start: 32 outliers final: 24 residues processed: 153 average time/residue: 0.1118 time to fit residues: 26.1168 Evaluate side-chains 153 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 35 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 17 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 chunk 121 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 170 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.080500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.055817 restraints weight = 64572.828| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 5.25 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15653 Z= 0.195 Angle : 0.642 10.754 21201 Z= 0.331 Chirality : 0.042 0.200 2190 Planarity : 0.004 0.048 2675 Dihedral : 7.131 68.661 2175 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.12 % Allowed : 17.31 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1751 helix: 1.48 (0.22), residues: 613 sheet: 0.14 (0.28), residues: 344 loop : -0.28 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 37 TYR 0.040 0.002 TYR E 18 PHE 0.015 0.002 PHE F 70 TRP 0.053 0.002 TRP G 70 HIS 0.009 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.19 (15633) covalent geometry : angle 0.63954 / 0.33 (21197) hydrogen bonds : bond 0.03515 / 2.34 ( 642) hydrogen bonds : angle 4.83422 / 3.36 ( 1845) metal coordination : bond 0.00900 / 0.60 ( 20) metal coordination : angle 3.96740 / 2.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.607 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: B 54 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7510 (tt0) REVERT: E 54 GLU cc_start: 0.5641 (tt0) cc_final: 0.5405 (tp30) REVERT: F 152 MET cc_start: 0.7445 (mtm) cc_final: 0.6653 (mtm) REVERT: F 193 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8292 (tt) REVERT: G 113 ASP cc_start: 0.7338 (p0) cc_final: 0.6915 (t0) REVERT: J 21 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8782 (tt) outliers start: 34 outliers final: 26 residues processed: 155 average time/residue: 0.1170 time to fit residues: 27.6890 Evaluate side-chains 151 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 80 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 110 optimal weight: 0.4980 chunk 23 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 27 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** 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 = 0.3983 r_free = 0.3983 target = 0.080945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.056373 restraints weight = 64104.877| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.90 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15653 Z= 0.172 Angle : 0.658 12.133 21201 Z= 0.336 Chirality : 0.042 0.219 2190 Planarity : 0.004 0.048 2675 Dihedral : 7.128 69.418 2175 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.88 % Allowed : 17.69 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1751 helix: 1.49 (0.22), residues: 613 sheet: 0.18 (0.28), residues: 342 loop : -0.29 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 37 TYR 0.034 0.001 TYR E 18 PHE 0.014 0.001 PHE F 70 TRP 0.045 0.002 TRP G 70 HIS 0.006 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (15633) covalent geometry : angle 0.65596 / 0.34 (21197) hydrogen bonds : bond 0.03432 / 2.28 ( 642) hydrogen bonds : angle 4.83128 / 3.35 ( 1845) metal coordination : bond 0.00759 / 0.51 ( 20) metal coordination : angle 3.83916 / 2.11 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7507 (tt0) REVERT: E 54 GLU cc_start: 0.5515 (tt0) cc_final: 0.5298 (tp30) REVERT: F 152 MET cc_start: 0.7471 (mtm) cc_final: 0.6696 (mtm) REVERT: F 193 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8317 (tt) REVERT: G 78 ASP cc_start: 0.6441 (OUTLIER) cc_final: 0.5901 (m-30) REVERT: G 113 ASP cc_start: 0.7281 (p0) cc_final: 0.6866 (t0) REVERT: H 87 ASP cc_start: 0.6909 (m-30) cc_final: 0.6663 (t70) REVERT: J 21 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8995 (tt) outliers start: 30 outliers final: 22 residues processed: 149 average time/residue: 0.1130 time to fit residues: 26.0916 Evaluate side-chains 148 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 142 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 0.5980 chunk 165 optimal weight: 20.0000 chunk 107 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS I 42 GLN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.081859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.057955 restraints weight = 64195.040| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.10 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15653 Z= 0.112 Angle : 0.631 12.224 21201 Z= 0.319 Chirality : 0.042 0.210 2190 Planarity : 0.004 0.050 2675 Dihedral : 6.989 71.022 2175 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.38 % Allowed : 18.00 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.20), residues: 1751 helix: 1.62 (0.22), residues: 612 sheet: 0.31 (0.28), residues: 339 loop : -0.19 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 33 TYR 0.031 0.001 TYR E 18 PHE 0.014 0.001 PHE J 77 TRP 0.040 0.002 TRP A 211 HIS 0.009 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (15633) covalent geometry : angle 0.62935 / 0.32 (21197) hydrogen bonds : bond 0.03077 / 2.02 ( 642) hydrogen bonds : angle 4.66679 / 3.25 ( 1845) metal coordination : bond 0.00425 / 0.28 ( 20) metal coordination : angle 3.45295 / 1.92 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3697.63 seconds wall clock time: 64 minutes 15.92 seconds (3855.92 seconds total)