Starting phenix.real_space_refine on Fri Jun 13 17:07:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cx1_27033/06_2025/8cx1_27033.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cx1_27033/06_2025/8cx1_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_27033/06_2025/8cx1_27033.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cx1_27033/06_2025/8cx1_27033.map" model { file = "/net/cci-nas-00/data/ceres_data/8cx1_27033/06_2025/8cx1_27033.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cx1_27033/06_2025/8cx1_27033.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15184 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3247 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 20, 'TRANS': 360} Chain: "B" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1468 Classifications: {'peptide': 176} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 166} Chain: "C" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1254 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "D" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "E" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 773 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain breaks: 1 Chain: "F" Number of atoms: 3228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3228 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 19, 'TRANS': 358} Chain breaks: 1 Chain: "G" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1468 Classifications: {'peptide': 176} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 166} Chain: "H" Number of atoms: 1261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1261 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 4, 'TRANS': 146} Chain: "I" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "J" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 761 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain breaks: 1 Chain: "K" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 168 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 3} Chain: "L" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 170 Classifications: {'RNA': 8} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 4, 'rna3p': 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2502 SG CYS A 288 42.030 21.534 43.933 1.00 47.72 S ATOM 2525 SG CYS A 291 42.651 24.950 44.112 1.00 37.27 S ATOM 869 SG CYS A 97 59.400 59.302 51.544 1.00 18.43 S ATOM 891 SG CYS A 100 62.215 59.354 53.235 1.00 18.86 S ATOM 4231 SG CYS B 114 32.654 86.941 53.193 1.00 36.79 S ATOM 4375 SG CYS B 133 36.263 86.031 54.456 1.00 38.93 S ATOM 9915 SG CYS F 288 37.805 24.096 99.023 1.00 69.54 S ATOM 9938 SG CYS F 291 38.741 27.149 98.924 1.00 57.72 S ATOM 8301 SG CYS F 97 38.650 65.124 88.704 1.00 32.31 S ATOM 8323 SG CYS F 100 36.226 66.030 87.464 1.00 34.28 S ATOM 11644 SG CYS G 114 74.484 78.383 86.004 1.00 74.52 S ATOM 11788 SG CYS G 133 70.979 78.633 84.619 1.00 73.68 S Time building chain proxies: 9.28, per 1000 atoms: 0.61 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: 3.67 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 257 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 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: 1.72 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: 4.04 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2397 1.31 - 1.43: 4688 1.43 - 1.56: 8378 1.56 - 1.69: 30 1.69 - 1.81: 140 Bond restraints: 15633 Sorted by residual: bond pdb=" CA ARG G 19 " pdb=" C ARG G 19 " ideal model delta sigma weight residual 1.524 1.463 0.061 1.26e-02 6.30e+03 2.35e+01 bond pdb=" CA TYR B 69 " pdb=" C TYR B 69 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.23e-02 6.61e+03 2.18e+01 bond pdb=" CA GLN B 83 " pdb=" C GLN B 83 " ideal model delta sigma weight residual 1.526 1.463 0.063 1.37e-02 5.33e+03 2.13e+01 bond pdb=" CA LYS G 22 " pdb=" C LYS G 22 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.27e-02 6.20e+03 1.99e+01 bond pdb=" CA ASP G 104 " pdb=" C ASP G 104 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.29e-02 6.01e+03 1.68e+01 ... (remaining 15628 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 20817 2.07 - 4.13: 327 4.13 - 6.20: 39 6.20 - 8.26: 12 8.26 - 10.33: 2 Bond angle restraints: 21197 Sorted by residual: angle pdb=" N ARG B 173 " pdb=" CA ARG B 173 " pdb=" C ARG B 173 " ideal model delta sigma weight residual 111.36 121.69 -10.33 1.09e+00 8.42e-01 8.98e+01 angle pdb=" N ILE B 18 " pdb=" CA ILE B 18 " pdb=" C ILE B 18 " ideal model delta sigma weight residual 110.42 118.09 -7.67 9.60e-01 1.09e+00 6.38e+01 angle pdb=" N ASP C 34 " pdb=" CA ASP C 34 " pdb=" C ASP C 34 " ideal model delta sigma weight residual 111.28 118.51 -7.23 1.09e+00 8.42e-01 4.40e+01 angle pdb=" N ASP H 34 " pdb=" CA ASP H 34 " pdb=" C ASP H 34 " ideal model delta sigma weight residual 111.75 119.48 -7.73 1.28e+00 6.10e-01 3.64e+01 angle pdb=" N ASN B 175 " pdb=" CA ASN B 175 " pdb=" C ASN B 175 " ideal model delta sigma weight residual 113.17 105.82 7.35 1.26e+00 6.30e-01 3.40e+01 ... (remaining 21192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 8267 17.52 - 35.04: 796 35.04 - 52.56: 170 52.56 - 70.07: 48 70.07 - 87.59: 16 Dihedral angle restraints: 9297 sinusoidal: 4064 harmonic: 5233 Sorted by residual: dihedral pdb=" CA GLU H 16 " pdb=" C GLU H 16 " pdb=" N PHE H 17 " pdb=" CA PHE H 17 " ideal model delta harmonic sigma weight residual 180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE C 17 " pdb=" C PHE C 17 " pdb=" N PHE C 18 " pdb=" CA PHE C 18 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU C 16 " pdb=" C GLU C 16 " pdb=" N PHE C 17 " pdb=" CA PHE C 17 " ideal model delta harmonic sigma weight residual 180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 9294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1968 0.072 - 0.143: 212 0.143 - 0.215: 7 0.215 - 0.287: 2 0.287 - 0.358: 1 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA ARG B 173 " pdb=" N ARG B 173 " pdb=" C ARG B 173 " pdb=" CB ARG B 173 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA PRO F 129 " pdb=" N PRO F 129 " pdb=" C PRO F 129 " pdb=" CB PRO F 129 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.20 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2187 not shown) Planarity restraints: 2675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 82 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLY G 82 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY G 82 " -0.026 2.00e-02 2.50e+03 pdb=" N GLN G 83 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 257 " 0.007 2.00e-02 2.50e+03 3.00e-02 1.35e+01 pdb=" CG HIS A 257 " 0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 257 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 HIS A 257 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS A 257 " 0.041 2.00e-02 2.50e+03 pdb=" NE2 HIS A 257 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 65 " 0.011 2.00e-02 2.50e+03 2.84e-02 1.21e+01 pdb=" CG HIS A 65 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS A 65 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 HIS A 65 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS A 65 " 0.041 2.00e-02 2.50e+03 pdb=" NE2 HIS A 65 " -0.008 2.00e-02 2.50e+03 ... (remaining 2672 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2914 2.78 - 3.31: 14567 3.31 - 3.84: 24469 3.84 - 4.37: 29376 4.37 - 4.90: 50293 Nonbonded interactions: 121619 Sorted by model distance: nonbonded pdb=" OG1 THR F 339 " pdb=" OE1 GLU F 342 " model vdw 2.244 3.040 nonbonded pdb=" N GLU E 56 " pdb=" OE1 GLU E 56 " model vdw 2.257 3.120 nonbonded pdb=" OG SER J 39 " pdb=" O LEU J 110 " model vdw 2.301 3.040 nonbonded pdb=" N GLU J 64 " pdb=" OE1 GLU J 64 " model vdw 2.303 3.120 nonbonded pdb=" O ASN B 3 " pdb=" OD1 ASN B 3 " model vdw 2.320 3.040 ... (remaining 121614 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 142 or resid 146 through 381 or resid 501 throug \ h 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: 34.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.490 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 15653 Z= 0.258 Angle : 0.654 10.328 21201 Z= 0.398 Chirality : 0.043 0.358 2190 Planarity : 0.004 0.063 2675 Dihedral : 14.846 87.593 5905 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (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 TRP 0.010 0.001 TRP B 5 HIS 0.046 0.002 HIS A 257 PHE 0.015 0.001 PHE J 77 TYR 0.013 0.001 TYR G 111 ARG 0.011 0.001 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.13438 ( 642) hydrogen bonds : angle 6.04382 ( 1845) metal coordination : bond 0.02901 ( 20) metal coordination : angle 5.54118 ( 4) covalent geometry : bond 0.00403 (15633) covalent geometry : angle 0.64937 (21197) *********************** 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 : 1.651 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: D 44 LEU cc_start: 0.7215 (mt) cc_final: 0.6919 (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: 0.3629 time to fit residues: 143.2324 Evaluate side-chains 160 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 1.802 ------------------------------------------------------------------------------- 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 146 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 0.0980 chunk 100 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS B 27 HIS ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.083256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.058174 restraints weight = 63116.551| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 5.27 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2443 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= 0.221 Angle : 0.674 8.624 21201 Z= 0.352 Chirality : 0.044 0.330 2190 Planarity : 0.005 0.043 2675 Dihedral : 8.167 67.431 2204 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.44 % Allowed : 9.38 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.20), residues: 1751 helix: 1.26 (0.21), residues: 625 sheet: -0.06 (0.27), residues: 333 loop : -0.48 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 211 HIS 0.007 0.001 HIS I 10 PHE 0.017 0.002 PHE J 62 TYR 0.024 0.002 TYR H 85 ARG 0.008 0.001 ARG F 374 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 642) hydrogen bonds : angle 5.32269 ( 1845) metal coordination : bond 0.00948 ( 20) metal coordination : angle 3.39012 ( 4) covalent geometry : bond 0.00495 (15633) covalent geometry : angle 0.67250 (21197) *********************** 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 202 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 1.899 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: C 7 ASP cc_start: 0.7068 (p0) cc_final: 0.6842 (p0) REVERT: C 18 PHE cc_start: 0.6941 (t80) cc_final: 0.6407 (t80) REVERT: C 20 LYS cc_start: 0.7922 (tptt) cc_final: 0.7702 (tptt) REVERT: D 32 GLU cc_start: 0.8602 (tt0) cc_final: 0.8259 (tp30) REVERT: E 32 LYS cc_start: 0.7347 (ttpp) cc_final: 0.7100 (mptt) REVERT: F 104 MET cc_start: 0.9120 (mtt) cc_final: 0.8913 (mtp) REVERT: F 227 MET cc_start: 0.7670 (mmm) cc_final: 0.6858 (mmm) REVERT: H 9 ARG cc_start: 0.9065 (ttt90) cc_final: 0.8817 (mtp-110) REVERT: H 127 PHE cc_start: 0.6376 (t80) cc_final: 0.6083 (t80) outliers start: 23 outliers final: 13 residues processed: 193 average time/residue: 0.2885 time to fit residues: 81.6762 Evaluate side-chains 164 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 12 MET Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain G residue 73 HIS 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 106 optimal weight: 0.9980 chunk 160 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 162 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.082954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.058192 restraints weight = 62811.197| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 5.08 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2891 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= 0.166 Angle : 0.606 7.625 21201 Z= 0.316 Chirality : 0.041 0.163 2190 Planarity : 0.004 0.046 2675 Dihedral : 8.050 69.210 2203 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.50 % Allowed : 11.50 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1751 helix: 1.48 (0.22), residues: 613 sheet: -0.01 (0.27), residues: 351 loop : -0.41 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 211 HIS 0.006 0.001 HIS I 10 PHE 0.014 0.001 PHE A 343 TYR 0.029 0.001 TYR E 18 ARG 0.005 0.000 ARG H 33 Details of bonding type rmsd hydrogen bonds : bond 0.03600 ( 642) hydrogen bonds : angle 5.10265 ( 1845) metal coordination : bond 0.00622 ( 20) metal coordination : angle 2.88464 ( 4) covalent geometry : bond 0.00374 (15633) covalent geometry : angle 0.60471 (21197) *********************** 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 187 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.854 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 146 GLN cc_start: 0.9001 (mt0) cc_final: 0.8696 (mp10) REVERT: C 18 PHE cc_start: 0.6768 (t80) cc_final: 0.6184 (t80) REVERT: C 19 ARG cc_start: 0.7515 (tpm170) cc_final: 0.7229 (tpp-160) REVERT: E 20 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8702 (tppp) REVERT: E 32 LYS cc_start: 0.7369 (ttpp) cc_final: 0.7164 (mttp) REVERT: G 70 TRP cc_start: 0.7212 (OUTLIER) cc_final: 0.6726 (m-10) REVERT: G 113 ASP cc_start: 0.7277 (p0) cc_final: 0.6814 (p0) REVERT: H 9 ARG cc_start: 0.9073 (ttt90) cc_final: 0.8809 (mtp-110) outliers start: 24 outliers final: 14 residues processed: 182 average time/residue: 0.2823 time to fit residues: 76.1783 Evaluate side-chains 152 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 94 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 129 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 112 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 27 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 = 0.4019 r_free = 0.4019 target = 0.082542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.057791 restraints weight = 62053.449| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 5.14 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3294 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= 0.158 Angle : 0.597 7.960 21201 Z= 0.311 Chirality : 0.041 0.205 2190 Planarity : 0.004 0.085 2675 Dihedral : 8.040 70.237 2203 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.88 % Allowed : 11.62 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1751 helix: 1.48 (0.22), residues: 617 sheet: -0.01 (0.27), residues: 356 loop : -0.37 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 211 HIS 0.006 0.001 HIS I 10 PHE 0.027 0.002 PHE F 262 TYR 0.016 0.001 TYR G 111 ARG 0.010 0.000 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 642) hydrogen bonds : angle 4.97497 ( 1845) metal coordination : bond 0.00718 ( 20) metal coordination : angle 2.57301 ( 4) covalent geometry : bond 0.00356 (15633) covalent geometry : angle 0.59604 (21197) *********************** 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 184 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 1.720 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 211 TRP cc_start: 0.8027 (p-90) cc_final: 0.7363 (p-90) REVERT: C 19 ARG cc_start: 0.7551 (tpm170) cc_final: 0.7249 (tpm170) REVERT: C 122 MET cc_start: 0.7586 (tpp) cc_final: 0.7377 (tpp) REVERT: E 20 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8749 (tppp) REVERT: E 32 LYS cc_start: 0.7212 (ttpp) cc_final: 0.6953 (mptt) REVERT: G 70 TRP cc_start: 0.7170 (OUTLIER) cc_final: 0.6680 (m-10) REVERT: G 78 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6444 (t0) REVERT: G 99 ASP cc_start: 0.8389 (t0) cc_final: 0.8103 (p0) REVERT: H 9 ARG cc_start: 0.9121 (ttt90) cc_final: 0.8761 (mtp180) outliers start: 30 outliers final: 20 residues processed: 175 average time/residue: 0.2943 time to fit residues: 75.3606 Evaluate side-chains 157 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 71 optimal weight: 8.9990 chunk 24 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 55 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN J 27 HIS ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.083862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.058351 restraints weight = 62975.596| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 5.21 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15653 Z= 0.107 Angle : 0.580 8.316 21201 Z= 0.299 Chirality : 0.041 0.193 2190 Planarity : 0.004 0.052 2675 Dihedral : 7.947 72.316 2203 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.44 % Allowed : 13.00 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.20), residues: 1751 helix: 1.63 (0.22), residues: 616 sheet: 0.28 (0.28), residues: 345 loop : -0.26 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 211 HIS 0.006 0.001 HIS I 10 PHE 0.033 0.001 PHE H 18 TYR 0.012 0.001 TYR J 18 ARG 0.008 0.000 ARG A 213 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 642) hydrogen bonds : angle 4.81414 ( 1845) metal coordination : bond 0.00305 ( 20) metal coordination : angle 2.48169 ( 4) covalent geometry : bond 0.00240 (15633) covalent geometry : angle 0.57890 (21197) *********************** 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 171 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 MET cc_start: 0.8960 (mmm) cc_final: 0.8756 (mmm) REVERT: B 2 GLU cc_start: 0.7541 (tp30) cc_final: 0.7329 (tp30) REVERT: C 19 ARG cc_start: 0.7460 (tpm170) cc_final: 0.7217 (tpm170) REVERT: E 20 LYS cc_start: 0.9032 (ttmm) cc_final: 0.8715 (tppp) REVERT: G 8 MET cc_start: 0.7703 (mmm) cc_final: 0.7501 (mmm) REVERT: G 70 TRP cc_start: 0.7001 (OUTLIER) cc_final: 0.6527 (m-10) REVERT: G 99 ASP cc_start: 0.8294 (t0) cc_final: 0.7998 (m-30) REVERT: H 29 TYR cc_start: 0.5875 (t80) cc_final: 0.5665 (t80) REVERT: H 127 PHE cc_start: 0.7106 (t80) cc_final: 0.6751 (t80) REVERT: J 21 LEU cc_start: 0.9212 (mt) cc_final: 0.8927 (pp) REVERT: J 29 PHE cc_start: 0.8036 (m-80) cc_final: 0.7641 (m-80) outliers start: 23 outliers final: 13 residues processed: 165 average time/residue: 0.2867 time to fit residues: 70.4031 Evaluate side-chains 148 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain G residue 134 GLU 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 J residue 28 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 93 optimal weight: 0.0570 chunk 16 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 168 optimal weight: 0.0570 chunk 35 optimal weight: 10.0000 overall best weight: 1.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** 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 = 0.4030 r_free = 0.4030 target = 0.083080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.058260 restraints weight = 63120.975| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 5.19 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15653 Z= 0.129 Angle : 0.569 9.467 21201 Z= 0.293 Chirality : 0.041 0.187 2190 Planarity : 0.004 0.048 2675 Dihedral : 7.927 71.384 2203 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.69 % Allowed : 13.56 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.20), residues: 1751 helix: 1.67 (0.22), residues: 616 sheet: 0.41 (0.28), residues: 342 loop : -0.23 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP F 211 HIS 0.006 0.001 HIS I 10 PHE 0.028 0.001 PHE F 262 TYR 0.025 0.001 TYR E 18 ARG 0.003 0.000 ARG A 226 Details of bonding type rmsd hydrogen bonds : bond 0.03154 ( 642) hydrogen bonds : angle 4.73743 ( 1845) metal coordination : bond 0.00500 ( 20) metal coordination : angle 2.43136 ( 4) covalent geometry : bond 0.00293 (15633) covalent geometry : angle 0.56838 (21197) *********************** 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 164 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 MET cc_start: 0.8156 (mmm) cc_final: 0.7889 (tpp) REVERT: E 20 LYS cc_start: 0.9023 (ttmm) cc_final: 0.8706 (tppp) REVERT: G 8 MET cc_start: 0.7873 (mmm) cc_final: 0.7636 (mmm) REVERT: G 70 TRP cc_start: 0.7049 (OUTLIER) cc_final: 0.6562 (m-10) REVERT: G 78 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6316 (t0) REVERT: G 99 ASP cc_start: 0.8376 (t0) cc_final: 0.7902 (m-30) REVERT: J 21 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9163 (pp) REVERT: J 29 PHE cc_start: 0.8288 (m-80) cc_final: 0.7979 (m-80) outliers start: 27 outliers final: 16 residues processed: 156 average time/residue: 0.2720 time to fit residues: 64.4720 Evaluate side-chains 143 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 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 70 TRP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 134 GLU 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 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 142 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 109 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 GLN ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.081134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.055898 restraints weight = 64160.035| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 5.29 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15653 Z= 0.214 Angle : 0.640 9.116 21201 Z= 0.332 Chirality : 0.042 0.194 2190 Planarity : 0.005 0.046 2675 Dihedral : 8.158 68.993 2203 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.19 % Allowed : 14.75 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1751 helix: 1.52 (0.22), residues: 613 sheet: 0.21 (0.27), residues: 350 loop : -0.20 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 211 HIS 0.007 0.001 HIS B 42 PHE 0.024 0.002 PHE H 18 TYR 0.024 0.002 TYR G 111 ARG 0.009 0.001 ARG C 19 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 642) hydrogen bonds : angle 4.86712 ( 1845) metal coordination : bond 0.00994 ( 20) metal coordination : angle 3.26819 ( 4) covalent geometry : bond 0.00475 (15633) covalent geometry : angle 0.63833 (21197) *********************** 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 173 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 138 time to evaluate : 2.381 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: B 101 GLU cc_start: 0.9063 (mp0) cc_final: 0.8842 (mp0) REVERT: C 18 PHE cc_start: 0.7282 (t80) cc_final: 0.6309 (t80) REVERT: E 18 TYR cc_start: 0.8148 (m-80) cc_final: 0.7935 (m-80) REVERT: E 20 LYS cc_start: 0.8970 (ttmm) cc_final: 0.8238 (tppp) REVERT: E 21 LEU cc_start: 0.9329 (mt) cc_final: 0.8625 (pp) REVERT: G 78 ASP cc_start: 0.6879 (OUTLIER) cc_final: 0.6420 (m-30) REVERT: H 46 ASN cc_start: 0.9394 (t0) cc_final: 0.9170 (t0) outliers start: 35 outliers final: 24 residues processed: 161 average time/residue: 0.2914 time to fit residues: 73.3460 Evaluate side-chains 152 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 3.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain 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 64 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 134 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 116 optimal weight: 0.9990 chunk 172 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 140 GLN ** 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 = 0.4023 r_free = 0.4023 target = 0.082395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.057742 restraints weight = 62703.809| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 5.13 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15653 Z= 0.124 Angle : 0.600 11.082 21201 Z= 0.306 Chirality : 0.042 0.214 2190 Planarity : 0.004 0.046 2675 Dihedral : 8.038 71.795 2203 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.38 % Allowed : 15.69 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.20), residues: 1751 helix: 1.64 (0.22), residues: 616 sheet: 0.41 (0.28), residues: 343 loop : -0.20 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 211 HIS 0.008 0.001 HIS B 80 PHE 0.019 0.001 PHE H 18 TYR 0.027 0.001 TYR E 18 ARG 0.002 0.000 ARG H 9 Details of bonding type rmsd hydrogen bonds : bond 0.03208 ( 642) hydrogen bonds : angle 4.66843 ( 1845) metal coordination : bond 0.00488 ( 20) metal coordination : angle 2.75859 ( 4) covalent geometry : bond 0.00281 (15633) covalent geometry : angle 0.59898 (21197) *********************** 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 158 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.823 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: C 18 PHE cc_start: 0.7244 (t80) cc_final: 0.6161 (t80) REVERT: E 17 MET cc_start: 0.4341 (tmm) cc_final: 0.3637 (tmm) REVERT: E 18 TYR cc_start: 0.8205 (m-80) cc_final: 0.7964 (m-80) REVERT: G 78 ASP cc_start: 0.6730 (OUTLIER) cc_final: 0.6272 (m-30) REVERT: H 46 ASN cc_start: 0.9390 (t0) cc_final: 0.9185 (t0) REVERT: J 21 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9221 (pp) REVERT: J 29 PHE cc_start: 0.8167 (m-80) cc_final: 0.7908 (m-80) REVERT: J 60 VAL cc_start: 0.7488 (OUTLIER) cc_final: 0.7160 (m) outliers start: 22 outliers final: 18 residues processed: 151 average time/residue: 0.2768 time to fit residues: 62.6385 Evaluate side-chains 151 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 265 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 116 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 112 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 158 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 73 optimal weight: 0.0870 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.081996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.057531 restraints weight = 62526.217| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 5.07 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15653 Z= 0.146 Angle : 0.610 11.381 21201 Z= 0.312 Chirality : 0.042 0.200 2190 Planarity : 0.004 0.051 2675 Dihedral : 8.047 71.300 2203 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.69 % Allowed : 15.38 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.20), residues: 1751 helix: 1.67 (0.22), residues: 612 sheet: 0.40 (0.28), residues: 342 loop : -0.16 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 211 HIS 0.009 0.001 HIS J 35 PHE 0.019 0.001 PHE H 18 TYR 0.025 0.001 TYR E 18 ARG 0.007 0.000 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 642) hydrogen bonds : angle 4.65696 ( 1845) metal coordination : bond 0.00614 ( 20) metal coordination : angle 2.72479 ( 4) covalent geometry : bond 0.00331 (15633) covalent geometry : angle 0.60903 (21197) *********************** 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 162 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7439 (tt0) REVERT: C 18 PHE cc_start: 0.7162 (t80) cc_final: 0.5972 (t80) REVERT: E 17 MET cc_start: 0.4339 (tmm) cc_final: 0.3735 (tmm) REVERT: E 18 TYR cc_start: 0.8229 (m-80) cc_final: 0.7999 (m-80) REVERT: F 227 MET cc_start: 0.7373 (tpp) cc_final: 0.7032 (mmm) REVERT: F 366 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.9119 (pm20) REVERT: G 78 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6215 (m-30) REVERT: J 21 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9259 (pp) REVERT: J 29 PHE cc_start: 0.8173 (m-80) cc_final: 0.7952 (m-80) REVERT: J 60 VAL cc_start: 0.7337 (OUTLIER) cc_final: 0.6920 (m) outliers start: 27 outliers final: 15 residues processed: 156 average time/residue: 0.2668 time to fit residues: 63.2065 Evaluate side-chains 153 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 366 GLU Chi-restraints excluded: chain G residue 78 ASP 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 J residue 21 LEU Chi-restraints excluded: chain J residue 28 GLU Chi-restraints excluded: chain J residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 123 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 20.0000 chunk 90 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 140 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN G 27 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.079436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.055118 restraints weight = 64739.691| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 5.14 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 15653 Z= 0.319 Angle : 0.756 17.337 21201 Z= 0.390 Chirality : 0.046 0.228 2190 Planarity : 0.005 0.048 2675 Dihedral : 8.499 67.581 2203 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.81 % Allowed : 16.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.20), residues: 1751 helix: 1.16 (0.21), residues: 614 sheet: 0.07 (0.28), residues: 350 loop : -0.41 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP A 211 HIS 0.007 0.002 HIS B 42 PHE 0.020 0.002 PHE F 70 TYR 0.033 0.002 TYR G 111 ARG 0.006 0.001 ARG F 169 Details of bonding type rmsd hydrogen bonds : bond 0.04201 ( 642) hydrogen bonds : angle 5.12738 ( 1845) metal coordination : bond 0.01512 ( 20) metal coordination : angle 3.85420 ( 4) covalent geometry : bond 0.00702 (15633) covalent geometry : angle 0.75376 (21197) ********************** 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 169 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 2.042 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: F 354 GLN cc_start: 0.8808 (tt0) cc_final: 0.8544 (tt0) REVERT: F 366 GLU cc_start: 0.9345 (OUTLIER) cc_final: 0.9112 (pm20) REVERT: G 78 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.6031 (m-30) REVERT: J 21 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9249 (pp) outliers start: 29 outliers final: 16 residues processed: 159 average time/residue: 0.3079 time to fit residues: 74.4916 Evaluate side-chains 153 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain E residue 65 ILE 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 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 103 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 3 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 136 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.082264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.057760 restraints weight = 63018.994| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 5.22 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15653 Z= 0.119 Angle : 0.644 12.212 21201 Z= 0.327 Chirality : 0.042 0.212 2190 Planarity : 0.004 0.050 2675 Dihedral : 8.179 73.486 2203 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.06 % Allowed : 17.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.20), residues: 1751 helix: 1.53 (0.21), residues: 613 sheet: 0.23 (0.28), residues: 345 loop : -0.19 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP G 70 HIS 0.008 0.001 HIS B 80 PHE 0.016 0.001 PHE A 343 TYR 0.016 0.001 TYR E 18 ARG 0.006 0.000 ARG I 37 Details of bonding type rmsd hydrogen bonds : bond 0.03221 ( 642) hydrogen bonds : angle 4.68417 ( 1845) metal coordination : bond 0.00441 ( 20) metal coordination : angle 2.69387 ( 4) covalent geometry : bond 0.00271 (15633) covalent geometry : angle 0.64289 (21197) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9282.46 seconds wall clock time: 163 minutes 37.23 seconds (9817.23 seconds total)