Starting phenix.real_space_refine on Sat Sep 12 10:20:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8cx1_27033/09_2026/8cx1_27033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cx1_27033/09_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_27033/09_2026/8cx1_27033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cx1_27033/09_2026/8cx1_27033.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8cx1_27033/09_2026/8cx1_27033.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8cx1_27033/09_2026/8cx1_27033.cif" model { file = "/net/cci-nas-00/data/ceres_data/8cx1_27033/09_2026/8cx1_27033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cx1_27033/09_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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 3.79, per 1000 atoms: 0.25 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: 1.32 Conformation dependent library (CDL) restraints added in 720.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 257 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 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: 0.42 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: 2.46 Time building geometry restraints manager: 1.76 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: 20747 2.07 - 4.13: 386 4.13 - 6.20: 49 6.20 - 8.26: 13 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: 8199 17.52 - 35.04: 819 35.04 - 52.56: 160 52.56 - 70.07: 66 70.07 - 87.59: 25 Dihedral angle restraints: 9269 sinusoidal: 4036 harmonic: 5233 Sorted by residual: dihedral pdb=" C4' A L 4 " pdb=" C3' A L 4 " pdb=" C2' A L 4 " pdb=" C1' A L 4 " ideal model delta sinusoidal sigma weight residual 36.34 -36.79 73.14 1 3.10e+00 1.04e-01 7.09e+02 dihedral pdb=" C4' U L 6 " pdb=" C3' U L 6 " pdb=" C2' U L 6 " pdb=" C1' U L 6 " ideal model delta sinusoidal sigma weight residual 36.34 -35.44 71.78 1 3.10e+00 1.04e-01 6.87e+02 dihedral pdb=" C4' U K 6 " pdb=" C3' U K 6 " pdb=" C2' U K 6 " pdb=" C1' U K 6 " ideal model delta sinusoidal sigma weight residual 36.34 -35.36 71.71 1 3.10e+00 1.04e-01 6.85e+02 ... (remaining 9266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1933 0.072 - 0.143: 213 0.143 - 0.215: 13 0.215 - 0.287: 30 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=" C2' U L 6 " pdb=" C3' U L 6 " pdb=" O2' U L 6 " pdb=" C1' U L 6 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' A K 4 " pdb=" C3' A K 4 " pdb=" O2' A K 4 " pdb=" C1' A K 4 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.95e+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: 3.900 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: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.730 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- 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= 0.259 Angle : 0.684 10.328 21201 Z= 0.405 Chirality : 0.052 0.358 2190 Planarity : 0.004 0.063 2675 Dihedral : 15.478 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 0.00407 / 0.26 (15633) covalent geometry : angle 0.67973 / 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 : 0.746 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: 0.1714 time to fit residues: 68.5928 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 : 0.577 ------------------------------------------------------------------------------- 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... ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.083373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.058889 restraints weight = 62519.266| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 5.19 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15653 Z= 0.211 Angle : 0.777 14.507 21201 Z= 0.381 Chirality : 0.062 0.975 2190 Planarity : 0.005 0.046 2675 Dihedral : 9.061 139.197 2176 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.31 % Allowed : 9.06 % Favored : 89.62 % 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: 0.34 (0.20), residues: 1751 helix: 1.30 (0.21), residues: 625 sheet: -0.02 (0.28), residues: 319 loop : -0.46 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 24 TYR 0.020 0.002 TYR G 111 PHE 0.017 0.002 PHE J 62 TRP 0.033 0.002 TRP F 211 HIS 0.007 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (15633) covalent geometry : angle 0.77524 / 0.38 (21197) hydrogen bonds : bond 0.04103 / 2.74 ( 642) hydrogen bonds : angle 5.30706 / 3.67 ( 1845) metal coordination : bond 0.00914 / 0.56 ( 20) metal coordination : angle 3.40149 / 1.82 ( 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 204 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 GLN cc_start: 0.9129 (mt0) cc_final: 0.8769 (mp10) REVERT: C 7 ASP cc_start: 0.7134 (p0) cc_final: 0.6902 (p0) REVERT: C 18 PHE cc_start: 0.6868 (t80) cc_final: 0.6400 (t80) REVERT: C 20 LYS cc_start: 0.7884 (tptt) cc_final: 0.7681 (tptt) REVERT: D 32 GLU cc_start: 0.8598 (tt0) cc_final: 0.8250 (tp30) REVERT: E 32 LYS cc_start: 0.7387 (ttpp) cc_final: 0.7106 (mptt) REVERT: F 227 MET cc_start: 0.7685 (mmm) cc_final: 0.6859 (mmm) REVERT: G 16 MET cc_start: 0.8367 (mpp) cc_final: 0.8117 (mpp) REVERT: H 127 PHE cc_start: 0.6479 (t80) cc_final: 0.6264 (t80) outliers start: 21 outliers final: 12 residues processed: 196 average time/residue: 0.1409 time to fit residues: 40.5079 Evaluate side-chains 161 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 263 LEU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain H residue 10 SER 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: 2.9990 chunk 129 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 69 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 HIS A 304 HIS B 73 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** J 27 HIS ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.083784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058996 restraints weight = 63145.365| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 5.09 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2932 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= 0.157 Angle : 0.661 8.346 21201 Z= 0.332 Chirality : 0.050 0.521 2190 Planarity : 0.004 0.047 2675 Dihedral : 9.098 139.949 2175 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.19 % Allowed : 11.94 % Favored : 86.88 % 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: 0.54 (0.20), residues: 1751 helix: 1.52 (0.22), residues: 613 sheet: 0.14 (0.28), residues: 344 loop : -0.40 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 213 TYR 0.044 0.001 TYR E 18 PHE 0.032 0.001 PHE F 262 TRP 0.031 0.002 TRP F 211 HIS 0.006 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (15633) covalent geometry : angle 0.65964 / 0.33 (21197) hydrogen bonds : bond 0.03548 / 2.37 ( 642) hydrogen bonds : angle 5.08017 / 3.52 ( 1845) metal coordination : bond 0.00521 / 0.32 ( 20) metal coordination : angle 2.77571 / 1.53 ( 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 182 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7504 (tpm170) cc_final: 0.7278 (tpp-160) REVERT: E 20 LYS cc_start: 0.9089 (ttmm) cc_final: 0.8771 (tppp) REVERT: G 99 ASP cc_start: 0.8102 (t0) cc_final: 0.7896 (p0) outliers start: 19 outliers final: 13 residues processed: 178 average time/residue: 0.1337 time to fit residues: 35.4398 Evaluate side-chains 154 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 129 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 162 optimal weight: 40.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.082536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.057794 restraints weight = 62287.455| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 5.12 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3360 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= 0.189 Angle : 0.664 8.423 21201 Z= 0.335 Chirality : 0.050 0.472 2190 Planarity : 0.004 0.041 2675 Dihedral : 9.077 140.275 2175 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.56 % Allowed : 12.19 % Favored : 86.25 % 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: 0.50 (0.20), residues: 1751 helix: 1.46 (0.22), residues: 617 sheet: 0.11 (0.28), residues: 348 loop : -0.40 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 320 TYR 0.041 0.002 TYR E 18 PHE 0.019 0.002 PHE H 18 TRP 0.031 0.002 TRP F 211 HIS 0.006 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (15633) covalent geometry : angle 0.66256 / 0.33 (21197) hydrogen bonds : bond 0.03497 / 2.33 ( 642) hydrogen bonds : angle 5.01798 / 3.49 ( 1845) metal coordination : bond 0.00733 / 0.44 ( 20) metal coordination : angle 3.00621 / 1.61 ( 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 178 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.7564 (tpm170) cc_final: 0.7290 (tpm170) REVERT: C 20 LYS cc_start: 0.7911 (tptt) cc_final: 0.7706 (tptt) REVERT: E 20 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8697 (tppp) REVERT: G 78 ASP cc_start: 0.6882 (OUTLIER) cc_final: 0.6357 (t0) REVERT: G 113 ASP cc_start: 0.7283 (p0) cc_final: 0.6901 (p0) REVERT: H 130 GLU cc_start: 0.8872 (mp0) cc_final: 0.8671 (pt0) outliers start: 25 outliers final: 18 residues processed: 171 average time/residue: 0.1342 time to fit residues: 34.2373 Evaluate side-chains 154 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 D residue 16 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 263 LEU 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 10 SER 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: 4.9990 chunk 17 optimal weight: 5.9990 chunk 165 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 172 optimal weight: 0.0770 overall best weight: 2.7744 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.082187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.056964 restraints weight = 63821.097| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 5.01 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3692 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= 0.186 Angle : 0.660 7.782 21201 Z= 0.333 Chirality : 0.049 0.444 2190 Planarity : 0.004 0.054 2675 Dihedral : 9.121 142.495 2175 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.69 % Allowed : 13.00 % Favored : 85.31 % 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: 0.52 (0.20), residues: 1751 helix: 1.46 (0.22), residues: 617 sheet: 0.11 (0.27), residues: 350 loop : -0.37 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 93 TYR 0.035 0.001 TYR E 18 PHE 0.033 0.002 PHE H 18 TRP 0.033 0.002 TRP F 211 HIS 0.006 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 (15633) covalent geometry : angle 0.65853 / 0.33 (21197) hydrogen bonds : bond 0.03508 / 2.34 ( 642) hydrogen bonds : angle 4.95984 / 3.45 ( 1845) metal coordination : bond 0.00921 / 0.51 ( 20) metal coordination : angle 2.86103 / 1.48 ( 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 168 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.613 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: C 18 PHE cc_start: 0.6963 (t80) cc_final: 0.6153 (t80) REVERT: C 19 ARG cc_start: 0.7590 (tpm170) cc_final: 0.7299 (tpm170) REVERT: C 20 LYS cc_start: 0.8009 (tptt) cc_final: 0.7791 (tptt) REVERT: E 20 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8736 (tppp) REVERT: J 21 LEU cc_start: 0.9218 (mt) cc_final: 0.8941 (pp) outliers start: 27 outliers final: 23 residues processed: 160 average time/residue: 0.1244 time to fit residues: 30.4351 Evaluate side-chains 154 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 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 12 MET Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 18 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 34 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 136 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 HIS ** 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** ** 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 = 0.4039 r_free = 0.4039 target = 0.083178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.058500 restraints weight = 63076.627| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 5.11 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.3899 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= 0.120 Angle : 0.624 10.648 21201 Z= 0.311 Chirality : 0.047 0.352 2190 Planarity : 0.004 0.045 2675 Dihedral : 8.987 140.700 2175 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.56 % Allowed : 14.12 % Favored : 84.31 % 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: 0.77 (0.20), residues: 1751 helix: 1.65 (0.22), residues: 616 sheet: 0.31 (0.28), residues: 345 loop : -0.23 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 226 TYR 0.030 0.001 TYR E 18 PHE 0.026 0.001 PHE H 18 TRP 0.034 0.001 TRP F 211 HIS 0.006 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (15633) covalent geometry : angle 0.62280 / 0.31 (21197) hydrogen bonds : bond 0.03147 / 2.08 ( 642) hydrogen bonds : angle 4.77262 / 3.30 ( 1845) metal coordination : bond 0.00426 / 0.28 ( 20) metal coordination : angle 2.80523 / 1.48 ( 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 167 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.647 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: E 20 LYS cc_start: 0.8922 (ttmm) cc_final: 0.8618 (tppp) REVERT: F 263 LEU cc_start: 0.9043 (mm) cc_final: 0.8445 (mm) REVERT: G 8 MET cc_start: 0.7801 (mmm) cc_final: 0.7582 (mmm) REVERT: G 78 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6303 (t0) REVERT: J 21 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8998 (pp) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 0.1212 time to fit residues: 29.8181 Evaluate side-chains 150 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 D residue 5 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 110 TYR 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 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: 0.3980 chunk 97 optimal weight: 6.9990 chunk 163 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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** F 304 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 = 0.4028 r_free = 0.4028 target = 0.082560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058098 restraints weight = 63233.123| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 5.09 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15653 Z= 0.141 Angle : 0.639 9.106 21201 Z= 0.319 Chirality : 0.047 0.316 2190 Planarity : 0.004 0.042 2675 Dihedral : 8.958 140.852 2175 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.69 % Allowed : 15.06 % Favored : 83.25 % 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: 0.77 (0.20), residues: 1751 helix: 1.62 (0.22), residues: 616 sheet: 0.31 (0.28), residues: 344 loop : -0.21 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.022 0.001 TYR E 18 PHE 0.020 0.001 PHE H 18 TRP 0.037 0.001 TRP F 211 HIS 0.006 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (15633) covalent geometry : angle 0.63844 / 0.32 (21197) hydrogen bonds : bond 0.03252 / 2.14 ( 642) hydrogen bonds : angle 4.71829 / 3.27 ( 1845) metal coordination : bond 0.00529 / 0.34 ( 20) metal coordination : angle 2.55833 / 1.34 ( 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: 27 poor density : 135 time to evaluate : 0.654 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: A 152 MET cc_start: 0.9026 (mmm) cc_final: 0.8647 (mtp) REVERT: B 8 MET cc_start: 0.8194 (mmm) cc_final: 0.7927 (tpp) REVERT: B 54 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7391 (tt0) REVERT: E 20 LYS cc_start: 0.8988 (ttmm) cc_final: 0.8280 (tppp) REVERT: E 21 LEU cc_start: 0.9305 (mt) cc_final: 0.8618 (pp) REVERT: F 263 LEU cc_start: 0.8987 (mm) cc_final: 0.8480 (mm) REVERT: G 8 MET cc_start: 0.7904 (mmm) cc_final: 0.7664 (mmm) REVERT: G 78 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6206 (t0) REVERT: J 21 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9134 (pp) outliers start: 27 outliers final: 22 residues processed: 153 average time/residue: 0.1246 time to fit residues: 29.2967 Evaluate side-chains 150 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 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 E residue 65 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 110 TYR 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 I residue 75 VAL 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: 2.9990 chunk 75 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 88 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.081731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.056823 restraints weight = 64067.653| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 5.24 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15653 Z= 0.192 Angle : 0.671 9.957 21201 Z= 0.335 Chirality : 0.049 0.349 2190 Planarity : 0.004 0.054 2675 Dihedral : 9.043 143.282 2175 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.00 % Allowed : 15.56 % Favored : 82.44 % 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: 0.73 (0.20), residues: 1751 helix: 1.59 (0.22), residues: 612 sheet: 0.23 (0.28), residues: 344 loop : -0.19 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 320 TYR 0.028 0.001 TYR E 18 PHE 0.028 0.002 PHE F 262 TRP 0.035 0.002 TRP F 211 HIS 0.006 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.19 (15633) covalent geometry : angle 0.66966 / 0.34 (21197) hydrogen bonds : bond 0.03436 / 2.27 ( 642) hydrogen bonds : angle 4.78744 / 3.31 ( 1845) metal coordination : bond 0.00845 / 0.52 ( 20) metal coordination : angle 2.96529 / 1.50 ( 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 165 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.749 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: 0.8099 (mt-10) cc_final: 0.7406 (tt0) REVERT: C 18 PHE cc_start: 0.7332 (t80) cc_final: 0.6270 (t80) REVERT: C 19 ARG cc_start: 0.7430 (tpm170) cc_final: 0.7202 (tpm170) REVERT: G 78 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6222 (m-30) REVERT: J 21 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8982 (pp) REVERT: J 60 VAL cc_start: 0.7314 (OUTLIER) cc_final: 0.6984 (m) outliers start: 32 outliers final: 24 residues processed: 153 average time/residue: 0.1274 time to fit residues: 29.7969 Evaluate side-chains 154 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 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 78 ASP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 134 GLU 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 I residue 75 VAL 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=1.50 ------------------------------------------------------------------------------- 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: 1.9990 chunk 121 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 154 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 90 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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** F 245 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.081986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.056813 restraints weight = 64330.489| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 4.90 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4367 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= 0.156 Angle : 0.662 14.063 21201 Z= 0.328 Chirality : 0.048 0.314 2190 Planarity : 0.004 0.048 2675 Dihedral : 9.021 143.304 2175 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.12 % Allowed : 16.06 % Favored : 81.81 % 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: 0.74 (0.20), residues: 1751 helix: 1.59 (0.22), residues: 613 sheet: 0.24 (0.28), residues: 345 loop : -0.19 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 37 TYR 0.027 0.001 TYR E 18 PHE 0.028 0.001 PHE F 262 TRP 0.033 0.001 TRP F 211 HIS 0.006 0.001 HIS I 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (15633) covalent geometry : angle 0.66133 / 0.33 (21197) hydrogen bonds : bond 0.03275 / 2.16 ( 642) hydrogen bonds : angle 4.72495 / 3.27 ( 1845) metal coordination : bond 0.00608 / 0.40 ( 20) metal coordination : angle 2.77786 / 1.43 ( 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 168 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.617 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: 0.8064 (mt-10) cc_final: 0.7479 (tt0) REVERT: F 366 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.8993 (pm20) REVERT: G 78 ASP cc_start: 0.6613 (OUTLIER) cc_final: 0.6122 (m-30) REVERT: H 87 ASP cc_start: 0.7018 (m-30) cc_final: 0.6649 (t70) REVERT: J 21 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9047 (pp) REVERT: J 60 VAL cc_start: 0.7324 (OUTLIER) cc_final: 0.7005 (m) outliers start: 34 outliers final: 24 residues processed: 156 average time/residue: 0.1273 time to fit residues: 30.3119 Evaluate side-chains 159 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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 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 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 265 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 134 GLU 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 108 VAL Chi-restraints excluded: chain I residue 75 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 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 110 optimal weight: 0.8980 chunk 23 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** F 245 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.082177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.057653 restraints weight = 64161.195| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 5.08 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15653 Z= 0.145 Angle : 0.677 12.048 21201 Z= 0.335 Chirality : 0.048 0.288 2190 Planarity : 0.004 0.049 2675 Dihedral : 9.019 142.875 2175 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.75 % Allowed : 16.44 % Favored : 81.81 % 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: 0.76 (0.20), residues: 1751 helix: 1.61 (0.22), residues: 612 sheet: 0.28 (0.28), residues: 342 loop : -0.19 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 37 TYR 0.027 0.001 TYR E 18 PHE 0.028 0.001 PHE F 262 TRP 0.039 0.001 TRP F 211 HIS 0.007 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (15633) covalent geometry : angle 0.67576 / 0.33 (21197) hydrogen bonds : bond 0.03218 / 2.11 ( 642) hydrogen bonds : angle 4.71225 / 3.26 ( 1845) metal coordination : bond 0.00552 / 0.37 ( 20) metal coordination : angle 2.71344 / 1.39 ( 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: 28 poor density : 130 time to evaluate : 0.648 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: A 338 MET cc_start: 0.8796 (mmm) cc_final: 0.8471 (mmm) REVERT: B 54 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7481 (tt0) REVERT: C 122 MET cc_start: 0.7613 (tpp) cc_final: 0.7124 (tpp) REVERT: F 227 MET cc_start: 0.7351 (tpp) cc_final: 0.7082 (mmm) REVERT: F 366 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.9106 (pm20) REVERT: G 78 ASP cc_start: 0.6570 (OUTLIER) cc_final: 0.6094 (m-30) REVERT: H 87 ASP cc_start: 0.7248 (m-30) cc_final: 0.6777 (t70) REVERT: H 122 MET cc_start: 0.8862 (tmm) cc_final: 0.8465 (tmm) REVERT: J 21 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9132 (pp) REVERT: J 60 VAL cc_start: 0.6997 (OUTLIER) cc_final: 0.6554 (m) outliers start: 28 outliers final: 21 residues processed: 148 average time/residue: 0.1218 time to fit residues: 28.0034 Evaluate side-chains 153 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 80 HIS Chi-restraints excluded: chain B residue 129 VAL 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 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 265 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 146 GLN 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 J residue 21 LEU Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 35 HIS 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: 3.9990 chunk 73 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 0.4980 chunk 165 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 0.0000 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.082999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.057924 restraints weight = 63756.567| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 5.12 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4493 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= 0.116 Angle : 0.669 12.770 21201 Z= 0.330 Chirality : 0.047 0.256 2190 Planarity : 0.004 0.050 2675 Dihedral : 8.978 141.182 2175 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.56 % Allowed : 16.44 % Favored : 82.00 % 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: 0.82 (0.20), residues: 1751 helix: 1.65 (0.22), residues: 612 sheet: 0.33 (0.28), residues: 336 loop : -0.15 (0.22), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 37 TYR 0.029 0.001 TYR E 18 PHE 0.029 0.001 PHE F 262 TRP 0.038 0.001 TRP F 211 HIS 0.012 0.001 HIS J 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (15633) covalent geometry : angle 0.66779 / 0.33 (21197) hydrogen bonds : bond 0.03018 / 1.98 ( 642) hydrogen bonds : angle 4.66256 / 3.22 ( 1845) metal coordination : bond 0.00350 / 0.23 ( 20) metal coordination : angle 2.49685 / 1.29 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4154.08 seconds wall clock time: 72 minutes 9.35 seconds (4329.35 seconds total)