Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 7 17:22:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/10_2023/8cx1_27033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/10_2023/8cx1_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_27033/10_2023/8cx1_27033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/10_2023/8cx1_27033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/10_2023/8cx1_27033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx1_27033/10_2023/8cx1_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-1.21rc1-5097/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: 7.86, per 1000 atoms: 0.52 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: 5.76 Conformation dependent library (CDL) restraints added in 2.1 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: 1.41 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: 4.19 Time building geometry restraints manager: 6.17 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: 8260 17.52 - 35.04: 794 35.04 - 52.56: 163 52.56 - 70.07: 36 70.07 - 87.59: 16 Dihedral angle restraints: 9269 sinusoidal: 4036 harmonic: 5233 Sorted by residual: dihedral pdb=" CA GLU H 16 " pdb=" C GLU H 16 " pdb=" N PHE H 17 " pdb=" CA PHE H 17 " ideal model delta harmonic sigma weight residual 180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE C 17 " pdb=" C PHE C 17 " pdb=" N PHE C 18 " pdb=" CA PHE C 18 " ideal model delta harmonic sigma weight residual 180.00 157.21 22.79 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLU C 16 " pdb=" C GLU C 16 " pdb=" N PHE C 17 " pdb=" CA PHE C 17 " ideal model delta harmonic sigma weight residual 180.00 -158.51 -21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 9266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1968 0.072 - 0.143: 212 0.143 - 0.215: 7 0.215 - 0.287: 2 0.287 - 0.358: 1 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA ARG B 173 " pdb=" N ARG B 173 " pdb=" C ARG B 173 " pdb=" CB ARG B 173 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA PRO F 129 " pdb=" N PRO F 129 " pdb=" C PRO F 129 " pdb=" CB PRO F 129 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ILE B 18 " pdb=" N ILE B 18 " pdb=" C ILE B 18 " pdb=" CB ILE B 18 " both_signs ideal model delta sigma weight residual False 2.43 2.20 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2187 not shown) Planarity restraints: 2675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY G 82 " -0.020 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C GLY G 82 " 0.068 2.00e-02 2.50e+03 pdb=" O GLY G 82 " -0.026 2.00e-02 2.50e+03 pdb=" N GLN G 83 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 257 " 0.007 2.00e-02 2.50e+03 3.00e-02 1.35e+01 pdb=" CG HIS A 257 " 0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 257 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 HIS A 257 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 HIS A 257 " 0.041 2.00e-02 2.50e+03 pdb=" NE2 HIS A 257 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 65 " 0.011 2.00e-02 2.50e+03 2.84e-02 1.21e+01 pdb=" CG HIS A 65 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS A 65 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 HIS A 65 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 HIS A 65 " 0.041 2.00e-02 2.50e+03 pdb=" NE2 HIS A 65 " -0.008 2.00e-02 2.50e+03 ... (remaining 2672 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2914 2.78 - 3.31: 14567 3.31 - 3.84: 24469 3.84 - 4.37: 29376 4.37 - 4.90: 50293 Nonbonded interactions: 121619 Sorted by model distance: nonbonded pdb=" OG1 THR F 339 " pdb=" OE1 GLU F 342 " model vdw 2.244 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: 2.490 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: 9.900 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 41.640 Find NCS groups from input model: 0.810 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.250 ------------------------------------------------------------------------------- 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 : 14.563 87.593 5877 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.06 % Allowed : 0.81 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 *********************** 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 : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 outliers start: 1 outliers final: 1 residues processed: 291 average time/residue: 0.3668 time to fit residues: 145.0613 Evaluate side-chains 158 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1286 time to fit residues: 2.6493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 44 optimal weight: 4.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 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: 3.0386 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15633 Z= 0.306 Angle : 0.661 8.551 21197 Z= 0.345 Chirality : 0.044 0.327 2190 Planarity : 0.005 0.042 2675 Dihedral : 6.808 66.859 2175 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.69 % Allowed : 10.19 % Favored : 88.12 % 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: 0.32 (0.20), residues: 1751 helix: 1.28 (0.21), residues: 625 sheet: -0.05 (0.27), residues: 348 loop : -0.45 (0.22), residues: 778 *********************** 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 201 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 174 time to evaluate : 1.910 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 outliers start: 27 outliers final: 15 residues processed: 190 average time/residue: 0.2906 time to fit residues: 80.9756 Evaluate side-chains 160 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1381 time to fit residues: 6.2562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 170 optimal weight: 0.0870 chunk 140 optimal weight: 3.9990 chunk 156 optimal weight: 20.0000 chunk 53 optimal weight: 0.0770 chunk 126 optimal weight: 6.9990 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 304 HIS C 140 GLN ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 HIS J 68 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15633 Z= 0.226 Angle : 0.595 13.408 21197 Z= 0.309 Chirality : 0.041 0.143 2190 Planarity : 0.004 0.078 2675 Dihedral : 6.791 67.884 2175 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.75 % Allowed : 12.06 % Favored : 87.19 % 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: 0.50 (0.20), residues: 1751 helix: 1.42 (0.22), residues: 629 sheet: 0.12 (0.27), residues: 348 loop : -0.39 (0.21), residues: 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3502 Ramachandran restraints generated. 1751 Oldfield, 0 Emsley, 1751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 163 time to evaluate : 2.112 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: 12 outliers final: 5 residues processed: 171 average time/residue: 0.2743 time to fit residues: 70.3058 Evaluate side-chains 139 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 1.685 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1339 time to fit residues: 3.5739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 82 optimal weight: 0.0470 chunk 149 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- 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 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS ** 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: 0.6755 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15633 Z= 0.258 Angle : 0.593 10.752 21197 Z= 0.308 Chirality : 0.041 0.139 2190 Planarity : 0.004 0.047 2675 Dihedral : 6.997 78.607 2175 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.19 % Allowed : 13.25 % 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: 0.54 (0.20), residues: 1751 helix: 1.46 (0.21), residues: 626 sheet: 0.10 (0.27), residues: 353 loop : -0.36 (0.21), residues: 772 *********************** 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 162 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.696 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: 19 outliers final: 12 residues processed: 151 average time/residue: 0.2700 time to fit residues: 61.5341 Evaluate side-chains 149 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1358 time to fit residues: 5.4724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 139 optimal weight: 0.0470 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 124 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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 12 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15633 Z= 0.224 Angle : 0.569 11.280 21197 Z= 0.298 Chirality : 0.040 0.187 2190 Planarity : 0.004 0.051 2675 Dihedral : 7.023 80.634 2175 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.00 % Allowed : 14.06 % Favored : 84.94 % 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: 0.64 (0.20), residues: 1751 helix: 1.49 (0.21), residues: 628 sheet: 0.15 (0.27), residues: 355 loop : -0.25 (0.22), residues: 768 *********************** 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 160 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 1.826 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 outliers start: 16 outliers final: 8 residues processed: 155 average time/residue: 0.3071 time to fit residues: 70.8606 Evaluate side-chains 140 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 132 time to evaluate : 1.790 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1558 time to fit residues: 4.6742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 138 optimal weight: 20.0000 chunk 77 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 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** ** E 68 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 8 GLN H 140 GLN ** 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: 0.6821 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15633 Z= 0.324 Angle : 0.622 10.794 21197 Z= 0.325 Chirality : 0.042 0.254 2190 Planarity : 0.004 0.048 2675 Dihedral : 7.253 85.576 2175 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.25 % Allowed : 15.69 % 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: 0.47 (0.20), residues: 1751 helix: 1.35 (0.21), residues: 629 sheet: -0.04 (0.27), residues: 358 loop : -0.29 (0.22), residues: 764 *********************** 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 154 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 134 time to evaluate : 1.699 Fit side-chains 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: 14 residues processed: 144 average time/residue: 0.2808 time to fit residues: 60.2168 Evaluate side-chains 140 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1755 time to fit residues: 6.4576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 140 optimal weight: 0.0370 chunk 93 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 104 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 76 optimal weight: 8.9990 overall best weight: 1.6862 ------------------------------------------------------------------------------- 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** ** E 68 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** ** 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: 0.6768 moved from start: 0.4016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15633 Z= 0.200 Angle : 0.582 11.128 21197 Z= 0.300 Chirality : 0.041 0.201 2190 Planarity : 0.004 0.045 2675 Dihedral : 7.173 85.676 2175 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.56 % Allowed : 15.94 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.20), residues: 1751 helix: 1.63 (0.22), residues: 617 sheet: 0.17 (0.27), residues: 350 loop : -0.23 (0.21), residues: 784 *********************** 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 145 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 1.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 140 average time/residue: 0.2658 time to fit residues: 57.1615 Evaluate side-chains 128 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 124 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1964 time to fit residues: 3.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 151 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 HIS ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 GLN ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.4130 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= 0.209 Angle : 0.588 11.934 21197 Z= 0.303 Chirality : 0.041 0.209 2190 Planarity : 0.005 0.145 2675 Dihedral : 7.126 79.688 2175 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.56 % Allowed : 17.00 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.21), residues: 629 sheet: 0.29 (0.28), residues: 344 loop : -0.27 (0.21), residues: 778 *********************** 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 143 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 140 average time/residue: 0.2705 time to fit residues: 58.0566 Evaluate side-chains 131 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1397 time to fit residues: 3.7545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 0.9980 chunk 145 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 140 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** ** E 68 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 ** 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: 0.6805 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15633 Z= 0.264 Angle : 0.621 12.745 21197 Z= 0.318 Chirality : 0.042 0.207 2190 Planarity : 0.004 0.048 2675 Dihedral : 7.222 76.322 2175 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.62 % Allowed : 17.31 % Favored : 82.06 % 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: 0.69 (0.20), residues: 1751 helix: 1.53 (0.21), residues: 629 sheet: 0.25 (0.28), residues: 344 loop : -0.26 (0.22), residues: 778 *********************** 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 138 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 132 average time/residue: 0.2719 time to fit residues: 55.7919 Evaluate side-chains 124 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 120 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1744 time to fit residues: 3.6920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 114 optimal weight: 0.9980 chunk 172 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 137 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15633 Z= 0.190 Angle : 0.597 12.754 21197 Z= 0.306 Chirality : 0.041 0.203 2190 Planarity : 0.004 0.049 2675 Dihedral : 7.112 71.613 2175 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.19 % Allowed : 17.50 % 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: 0.81 (0.20), residues: 1751 helix: 1.61 (0.21), residues: 629 sheet: 0.40 (0.28), residues: 329 loop : -0.21 (0.21), residues: 793 ********************** 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 135 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 134 average time/residue: 0.2796 time to fit residues: 57.8448 Evaluate side-chains 126 residues out of total 1600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 123 time to evaluate : 1.842 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1509 time to fit residues: 3.3459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 HIS ** G 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.080101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.055337 restraints weight = 63412.236| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 5.16 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15633 Z= 0.354 Angle : 0.679 11.716 21197 Z= 0.354 Chirality : 0.043 0.232 2190 Planarity : 0.005 0.049 2675 Dihedral : 7.378 70.099 2175 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.38 % Allowed : 17.94 % Favored : 81.69 % 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: 0.55 (0.20), residues: 1751 helix: 1.41 (0.21), residues: 627 sheet: 0.12 (0.28), residues: 345 loop : -0.30 (0.22), residues: 779 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3037.87 seconds wall clock time: 56 minutes 17.67 seconds (3377.67 seconds total)