Starting phenix.real_space_refine on Fri Feb 16 11:24:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/02_2024/8cx1_27033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/02_2024/8cx1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/02_2024/8cx1_27033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/02_2024/8cx1_27033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/02_2024/8cx1_27033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/02_2024/8cx1_27033.pdb" } 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 Residue "A GLU 10": "OE1" <-> "OE2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "F PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F ASP 103": "OD1" <-> "OD2" Residue "F PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "G TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.70, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 6.07 Conformation dependent library (CDL) restraints added in 2.8 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: 1.64 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: 4.43 Time building geometry restraints manager: 6.56 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: 99.70 - 106.58: 609 106.58 - 113.46: 8109 113.46 - 120.34: 5967 120.34 - 127.22: 6226 127.22 - 134.09: 286 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 2.440 nonbonded pdb=" N GLU E 56 " pdb=" OE1 GLU E 56 " model vdw 2.257 2.520 nonbonded pdb=" OG SER J 39 " pdb=" O LEU J 110 " model vdw 2.301 2.440 nonbonded pdb=" N GLU J 64 " pdb=" OE1 GLU J 64 " model vdw 2.303 2.520 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 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: 1.860 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: 9.810 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 43.330 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.420 ------------------------------------------------------------------------------- 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 0.063 15633 Z= 0.262 Angle : 0.649 10.328 21197 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 1.596 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: 0.3503 time to fit residues: 137.8289 Evaluate side-chains 160 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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: 3.9990 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 135 optimal weight: 0.0470 chunk 52 optimal weight: 7.9990 chunk 82 optimal weight: 0.1980 chunk 100 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 overall best weight: 2.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN G 175 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15633 Z= 0.301 Angle : 0.656 8.648 21197 Z= 0.342 Chirality : 0.043 0.317 2190 Planarity : 0.004 0.043 2675 Dihedral : 8.105 67.891 2204 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.56 % Allowed : 9.81 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.36 (0.20), residues: 1751 helix: 1.30 (0.21), residues: 625 sheet: -0.02 (0.27), residues: 348 loop : -0.44 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 211 HIS 0.008 0.001 HIS A 4 PHE 0.017 0.002 PHE J 62 TYR 0.026 0.002 TYR H 85 ARG 0.007 0.001 ARG F 374 *********************** 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 fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 2.236 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 18 PHE cc_start: 0.5372 (t80) cc_final: 0.5078 (t80) REVERT: E 32 LYS cc_start: 0.7599 (ttpp) cc_final: 0.7315 (mptt) outliers start: 25 outliers final: 15 residues processed: 192 average time/residue: 0.2974 time to fit residues: 82.8413 Evaluate side-chains 166 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain G residue 61 ASP 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 87 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 157 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 140 optimal weight: 9.9990 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 0.0040 chunk 126 optimal weight: 1.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- 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** C 140 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 HIS F 216 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15633 Z= 0.194 Angle : 0.582 7.983 21197 Z= 0.303 Chirality : 0.041 0.148 2190 Planarity : 0.004 0.084 2675 Dihedral : 7.982 70.000 2203 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.25 % Allowed : 12.31 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.20), residues: 1751 helix: 1.48 (0.22), residues: 625 sheet: 0.14 (0.27), residues: 348 loop : -0.34 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 211 HIS 0.007 0.001 HIS J 35 PHE 0.015 0.001 PHE A 343 TYR 0.037 0.001 TYR E 18 ARG 0.008 0.000 ARG A 213 *********************** 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 183 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 2.219 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 outliers start: 20 outliers final: 13 residues processed: 177 average time/residue: 0.2726 time to fit residues: 72.3001 Evaluate side-chains 150 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain G residue 61 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 250 HIS A 304 HIS ** 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 37 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6720 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15633 Z= 0.224 Angle : 0.579 8.915 21197 Z= 0.302 Chirality : 0.040 0.152 2190 Planarity : 0.004 0.037 2675 Dihedral : 8.093 80.745 2203 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.94 % Allowed : 12.81 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.20), residues: 1751 helix: 1.55 (0.21), residues: 625 sheet: 0.16 (0.27), residues: 353 loop : -0.30 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 211 HIS 0.006 0.001 HIS I 10 PHE 0.027 0.002 PHE F 262 TYR 0.042 0.001 TYR E 18 ARG 0.012 0.000 ARG H 52 *********************** 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 176 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 145 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7096 (p-80) REVERT: H 18 PHE cc_start: 0.4180 (OUTLIER) cc_final: 0.2203 (t80) outliers start: 31 outliers final: 23 residues processed: 164 average time/residue: 0.2576 time to fit residues: 64.1197 Evaluate side-chains 154 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS 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 120 ILE 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 D residue 53 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain H residue 18 PHE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 150 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 ASN ** 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 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 GLN ** J 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 15633 Z= 0.331 Angle : 0.630 9.606 21197 Z= 0.333 Chirality : 0.042 0.179 2190 Planarity : 0.004 0.051 2675 Dihedral : 8.285 78.825 2203 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.56 % Allowed : 14.25 % Favored : 83.19 % 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: 0.46 (0.20), residues: 1751 helix: 1.32 (0.21), residues: 626 sheet: 0.06 (0.27), residues: 358 loop : -0.33 (0.22), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 211 HIS 0.008 0.001 HIS B 42 PHE 0.020 0.002 PHE H 18 TYR 0.029 0.002 TYR E 18 ARG 0.007 0.001 ARG A 320 *********************** 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 174 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 133 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7117 (p-80) REVERT: C 18 PHE cc_start: 0.5420 (t80) cc_final: 0.4847 (t80) REVERT: H 46 ASN cc_start: 0.8455 (t0) cc_final: 0.8241 (t0) REVERT: J 75 MET cc_start: 0.6471 (mmt) cc_final: 0.6264 (tpp) outliers start: 41 outliers final: 27 residues processed: 162 average time/residue: 0.2450 time to fit residues: 61.4547 Evaluate side-chains 148 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 120 ILE 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 D residue 47 ASP Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 230 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 108 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 87 optimal weight: 0.0040 overall best weight: 1.9598 ------------------------------------------------------------------------------- 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 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** J 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15633 Z= 0.211 Angle : 0.581 10.316 21197 Z= 0.302 Chirality : 0.041 0.176 2190 Planarity : 0.004 0.042 2675 Dihedral : 8.214 81.624 2203 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.12 % Allowed : 14.81 % 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: 0.67 (0.20), residues: 1751 helix: 1.54 (0.21), residues: 628 sheet: 0.17 (0.27), residues: 358 loop : -0.25 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP G 70 HIS 0.007 0.001 HIS I 10 PHE 0.034 0.002 PHE H 18 TYR 0.033 0.001 TYR E 18 ARG 0.004 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 HIS cc_start: 0.7857 (OUTLIER) cc_final: 0.7082 (p-80) REVERT: C 18 PHE cc_start: 0.5374 (t80) cc_final: 0.4718 (t80) REVERT: G 66 ILE cc_start: 0.8339 (mp) cc_final: 0.8100 (mt) REVERT: J 75 MET cc_start: 0.6432 (mmt) cc_final: 0.6125 (tpp) outliers start: 34 outliers final: 26 residues processed: 159 average time/residue: 0.2455 time to fit residues: 60.7757 Evaluate side-chains 149 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 120 ILE 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 47 ASP Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 111 ASP Chi-restraints excluded: chain F residue 216 HIS Chi-restraints excluded: chain F residue 229 ASN Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain G residue 170 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 40.0000 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 0.1980 chunk 166 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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** F 304 HIS G 12 GLN J 27 HIS J 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15633 Z= 0.155 Angle : 0.572 10.809 21197 Z= 0.293 Chirality : 0.040 0.183 2190 Planarity : 0.004 0.045 2675 Dihedral : 8.159 88.521 2203 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.88 % Allowed : 15.81 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1751 helix: 1.69 (0.21), residues: 627 sheet: 0.38 (0.28), residues: 352 loop : -0.18 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 211 HIS 0.006 0.001 HIS A 4 PHE 0.018 0.001 PHE H 18 TYR 0.017 0.001 TYR E 18 ARG 0.005 0.000 ARG A 213 *********************** 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 168 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 138 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7121 (p-80) REVERT: F 263 LEU cc_start: 0.7508 (mm) cc_final: 0.7207 (mm) REVERT: G 66 ILE cc_start: 0.8319 (mp) cc_final: 0.8074 (mt) REVERT: J 60 VAL cc_start: 0.5095 (OUTLIER) cc_final: 0.4774 (m) REVERT: J 75 MET cc_start: 0.6367 (mmt) cc_final: 0.6082 (tpp) outliers start: 30 outliers final: 21 residues processed: 160 average time/residue: 0.2410 time to fit residues: 59.7233 Evaluate side-chains 147 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 120 ILE 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 E residue 111 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain G residue 110 TYR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 103 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.4980 chunk 66 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15633 Z= 0.247 Angle : 0.607 13.149 21197 Z= 0.311 Chirality : 0.041 0.170 2190 Planarity : 0.004 0.053 2675 Dihedral : 8.233 88.819 2203 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.19 % Allowed : 16.38 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.62 (0.21), residues: 627 sheet: 0.39 (0.28), residues: 350 loop : -0.20 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 211 HIS 0.021 0.001 HIS J 35 PHE 0.037 0.002 PHE J 29 TYR 0.016 0.001 TYR G 111 ARG 0.014 0.000 ARG I 37 *********************** 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 161 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7152 (p-80) REVERT: J 75 MET cc_start: 0.6421 (mmt) cc_final: 0.6128 (tpp) outliers start: 35 outliers final: 27 residues processed: 149 average time/residue: 0.2546 time to fit residues: 57.8306 Evaluate side-chains 146 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 150 LEU 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 D residue 53 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain G residue 98 VAL 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 I residue 75 VAL Chi-restraints excluded: chain J residue 28 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 93 optimal weight: 0.5980 chunk 67 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 140 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 245 GLN ** G 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15633 Z= 0.288 Angle : 0.627 11.730 21197 Z= 0.323 Chirality : 0.041 0.232 2190 Planarity : 0.004 0.049 2675 Dihedral : 8.315 83.711 2203 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.31 % Allowed : 16.50 % Favored : 81.19 % 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: 0.74 (0.20), residues: 1751 helix: 1.54 (0.21), residues: 627 sheet: 0.40 (0.28), residues: 344 loop : -0.25 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 211 HIS 0.008 0.001 HIS I 10 PHE 0.024 0.002 PHE J 29 TYR 0.021 0.002 TYR G 111 ARG 0.008 0.000 ARG A 213 *********************** 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 158 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 121 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7520 (p-80) REVERT: B 8 MET cc_start: 0.6231 (tpp) cc_final: 0.5747 (tpt) REVERT: J 75 MET cc_start: 0.6410 (mmt) cc_final: 0.6101 (tpp) outliers start: 37 outliers final: 31 residues processed: 147 average time/residue: 0.2384 time to fit residues: 55.1985 Evaluate side-chains 152 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 55 ILE Chi-restraints excluded: chain H residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 114 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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** C 140 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 GLN ** G 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 HIS ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6904 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15633 Z= 0.447 Angle : 0.710 10.192 21197 Z= 0.371 Chirality : 0.044 0.214 2190 Planarity : 0.005 0.048 2675 Dihedral : 8.625 81.770 2203 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.50 % Allowed : 16.25 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.20), residues: 1751 helix: 1.12 (0.21), residues: 627 sheet: 0.10 (0.27), residues: 358 loop : -0.41 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 211 HIS 0.009 0.002 HIS I 10 PHE 0.025 0.002 PHE J 29 TYR 0.032 0.002 TYR G 111 ARG 0.005 0.001 ARG F 313 ********************** 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 168 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 MET cc_start: 0.6321 (tpp) cc_final: 0.5937 (tpt) REVERT: C 18 PHE cc_start: 0.5599 (t80) cc_final: 0.4876 (t80) REVERT: J 45 MET cc_start: 0.1850 (ppp) cc_final: 0.0781 (mtt) outliers start: 40 outliers final: 34 residues processed: 157 average time/residue: 0.2509 time to fit residues: 60.3795 Evaluate side-chains 152 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 HIS Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain C residue 103 LEU Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 53 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 67 GLU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain G residue 8 MET Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 61 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 70 TRP Chi-restraints excluded: chain G residue 146 GLN Chi-restraints excluded: chain G residue 170 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 17 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.080907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3390 r_free = 0.3390 target = 0.056116 restraints weight = 65118.396| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 5.34 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15633 Z= 0.232 Angle : 0.630 11.139 21197 Z= 0.326 Chirality : 0.042 0.205 2190 Planarity : 0.004 0.081 2675 Dihedral : 8.401 76.490 2203 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.00 % Allowed : 16.94 % Favored : 81.06 % 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: 0.60 (0.20), residues: 1751 helix: 1.45 (0.21), residues: 615 sheet: 0.28 (0.28), residues: 344 loop : -0.32 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 211 HIS 0.009 0.001 HIS I 10 PHE 0.020 0.002 PHE J 29 TYR 0.018 0.001 TYR G 111 ARG 0.013 0.000 ARG D 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3270.36 seconds wall clock time: 60 minutes 11.54 seconds (3611.54 seconds total)