Starting phenix.real_space_refine on Tue Apr 9 02:01:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx2_27034/04_2024/8cx2_27034.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx2_27034/04_2024/8cx2_27034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx2_27034/04_2024/8cx2_27034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx2_27034/04_2024/8cx2_27034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx2_27034/04_2024/8cx2_27034.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cx2_27034/04_2024/8cx2_27034.pdb" } resolution = 3.2 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= 0.001 sd= 0.039 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 18 5.49 5 S 92 5.16 5 C 9525 2.51 5 N 2668 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 130": "OD1" <-> "OD2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 26": "OE1" <-> "OE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 26": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15041 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3211 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 19, 'TRANS': 357} 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: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 698 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "E" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "F" Number of atoms: 3211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3211 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 19, 'TRANS': 357} 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: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1275 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} 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: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain breaks: 1 Chain: "K" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 4} Link IDs: {'rna2p': 4, 'rna3p': 4} Chain: "L" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 2} Link IDs: {'rna2p': 4, 'rna3p': 4} 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 2457 SG CYS A 288 34.823 21.522 36.834 1.00104.36 S ATOM 2480 SG CYS A 291 35.490 24.180 37.316 1.00 93.76 S ATOM 824 SG CYS A 97 55.944 55.618 50.636 1.00 46.37 S ATOM 846 SG CYS A 100 58.143 55.092 52.191 1.00 56.54 S ATOM 4195 SG CYS B 114 32.332 86.770 53.473 1.00 94.58 S ATOM 4339 SG CYS B 133 35.703 85.325 54.750 1.00 90.36 S ATOM 9776 SG CYS F 288 18.165 56.352 107.513 1.00132.85 S ATOM 9799 SG CYS F 291 21.029 56.636 106.539 1.00124.22 S ATOM 8143 SG CYS F 97 51.398 67.782 84.004 1.00 49.52 S ATOM 8165 SG CYS F 100 50.987 70.212 82.350 1.00 58.78 S ATOM 11514 SG CYS G 114 76.648 38.602 81.181 1.00162.59 S ATOM 11658 SG CYS G 133 75.213 41.532 79.251 1.00156.40 S Time building chain proxies: 8.06, per 1000 atoms: 0.54 Number of scatterers: 15041 At special positions: 0 Unit cell: (136.105, 140.28, 138.61, 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 92 16.00 P 18 15.00 O 2732 8.00 N 2668 7.00 C 9525 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: 5.83 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 288 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 291 " pdb=" ZN A 502 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 502 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 502 " - pdb=" ND1 HIS A 65 " 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 114 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 133 " pdb=" ZN F 501 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 291 " pdb="ZN ZN F 501 " - pdb=" ND1 HIS F 257 " pdb="ZN ZN F 501 " - pdb=" SG CYS F 288 " pdb=" ZN F 502 " pdb="ZN ZN F 502 " - pdb=" ND1 HIS F 65 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 100 " pdb="ZN ZN F 502 " - pdb=" SG CYS F 97 " 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 114 " pdb="ZN ZN G 201 " - pdb=" SG CYS G 133 " Number of angles added : 4 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 13 sheets defined 40.1% alpha, 21.1% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 4.47 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: 3.664A pdb=" N LYS A 76 " --> pdb=" O HIS A 72 " (cutoff:3.500A) 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 removed outlier: 3.598A pdb=" N LYS A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) No H-bonds generated for '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 removed outlier: 4.000A pdb=" N GLU A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 351 removed outlier: 3.631A 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: 3.613A pdb=" N GLU B 45 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 46 " --> pdb=" O HIS B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 42 through 46' Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.765A 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 16 removed outlier: 4.362A pdb=" N GLU C 16 " --> pdb=" O PHE C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 51 Processing helix chain 'C' and resid 71 through 75 Processing helix chain 'C' and resid 129 through 135 removed outlier: 4.434A pdb=" N GLN C 133 " --> pdb=" O GLU C 129 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 149 Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.640A pdb=" N GLY D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 4.478A 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 33 through 38 removed outlier: 3.682A pdb=" N THR E 38 " --> pdb=" O GLU E 34 " (cutoff:3.500A) 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: 4.407A pdb=" N LEU E 101 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 22 removed outlier: 3.809A 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 78 removed outlier: 3.821A pdb=" N LYS F 76 " --> pdb=" O HIS F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 111 Processing helix chain 'F' and resid 128 through 140 Processing helix chain 'F' and resid 153 through 165 removed outlier: 3.728A pdb=" N VAL F 165 " --> pdb=" O TRP F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 194 Processing helix chain 'F' and resid 198 through 207 removed outlier: 3.965A pdb=" N ASN F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) 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 320 through 332 removed outlier: 3.547A pdb=" N GLY F 324 " --> pdb=" O ARG F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 351 removed outlier: 3.654A pdb=" N VAL F 351 " --> pdb=" O TRP F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 381 removed outlier: 3.567A pdb=" N ASN F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 31 Processing helix chain 'G' and resid 32 through 36 removed outlier: 4.288A pdb=" N ALA G 35 " --> pdb=" O SER G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 109 Processing helix chain 'G' and resid 118 through 126 Processing helix chain 'G' and resid 135 through 140 removed outlier: 3.949A pdb=" N ASN G 140 " --> pdb=" O ALA G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 154 Processing helix chain 'G' and resid 165 through 170 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 36 through 51 Processing helix chain 'H' and resid 129 through 135 removed outlier: 4.411A pdb=" N GLN H 133 " --> pdb=" O GLU H 129 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLN H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 147 Processing helix chain 'I' and resid 23 through 36 removed outlier: 3.573A pdb=" N GLY I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 4.224A 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 38 removed outlier: 3.836A pdb=" N THR J 38 " --> pdb=" O GLU J 34 " (cutoff:3.500A) 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: 4.168A pdb=" N LEU J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 5.203A 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 54 removed outlier: 3.720A pdb=" N ASP A 50 " --> pdb=" O VAL A 39 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N TRP A 94 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N THR A 148 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 116 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LYS A 150 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.070A 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: 5.144A pdb=" N VAL A 224 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N GLN A 237 " --> pdb=" O TYR A 222 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N TYR A 222 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N ARG A 239 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 11.769A pdb=" N LEU A 220 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.819A pdb=" N ASP C 120 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.746A pdb=" N GLY B 84 " --> pdb=" O TYR B 69 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 62 " --> pdb=" O PRO B 58 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B 64 " --> pdb=" O HIS B 56 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N HIS B 56 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE B 66 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU B 54 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.463A 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 Processing sheet with id=AA6, first strand: chain 'D' and resid 43 through 45 removed outlier: 3.865A pdb=" N ALA D 73 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL D 75 " --> pdb=" O MET D 6 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 8 " --> pdb=" O VAL D 75 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 77 " --> pdb=" O ARG D 8 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 15 " --> pdb=" O ILE E 30 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYS E 32 " --> pdb=" O PHE D 15 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N ASP D 17 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS E 27 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 8.744A pdb=" N VAL E 60 " --> pdb=" O TYR E 18 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS E 20 " --> pdb=" O VAL E 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 8 through 9 removed outlier: 3.732A pdb=" N ASP F 50 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 231 through 243 removed outlier: 8.903A pdb=" N LEU F 234 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 9.439A pdb=" N HIS F 228 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N ASN F 236 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 11.642A pdb=" N ARG F 226 " --> pdb=" O ASN F 236 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG F 238 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N TYR F 219 " --> pdb=" O SER F 284 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER F 284 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N TRP F 285 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS F 334 " --> pdb=" O LEU F 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 5 through 9 removed outlier: 3.643A pdb=" N ASP H 120 " --> pdb=" O ASP H 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR H 85 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.837A pdb=" N VAL G 13 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN G 83 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA G 62 " --> pdb=" O PRO G 58 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU G 64 " --> pdb=" O HIS G 56 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N HIS G 56 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE G 66 " --> pdb=" O GLU G 54 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU G 54 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR G 68 " --> pdb=" O SER G 52 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 13 removed outlier: 3.837A pdb=" N VAL G 13 " --> pdb=" O GLN G 83 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN G 83 " --> pdb=" O VAL G 13 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 12 through 18 removed outlier: 4.119A pdb=" N ALA I 73 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET I 6 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL I 75 " --> pdb=" O MET I 6 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG I 8 " --> pdb=" O VAL I 75 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU I 77 " --> pdb=" O ARG I 8 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU I 44 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 28 through 32 668 hydrogen bonds defined for protein. 1902 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 6.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2590 1.32 - 1.45: 4479 1.45 - 1.57: 8253 1.57 - 1.69: 34 1.69 - 1.81: 134 Bond restraints: 15490 Sorted by residual: bond pdb=" CA ASP G 104 " pdb=" C ASP G 104 " ideal model delta sigma weight residual 1.524 1.474 0.050 1.32e-02 5.74e+03 1.43e+01 bond pdb=" CA HIS B 80 " pdb=" C HIS B 80 " ideal model delta sigma weight residual 1.524 1.482 0.042 1.26e-02 6.30e+03 1.12e+01 bond pdb=" CA TRP G 70 " pdb=" C TRP G 70 " ideal model delta sigma weight residual 1.523 1.485 0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" CA THR B 20 " pdb=" C THR B 20 " ideal model delta sigma weight residual 1.524 1.486 0.038 1.29e-02 6.01e+03 8.51e+00 bond pdb=" C ASP G 104 " pdb=" O ASP G 104 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.22e-02 6.72e+03 8.31e+00 ... (remaining 15485 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.48: 596 106.48 - 113.39: 8064 113.39 - 120.31: 5841 120.31 - 127.22: 6228 127.22 - 134.14: 292 Bond angle restraints: 21021 Sorted by residual: angle pdb=" N HIS B 80 " pdb=" CA HIS B 80 " pdb=" C HIS B 80 " ideal model delta sigma weight residual 111.14 105.94 5.20 1.08e+00 8.57e-01 2.32e+01 angle pdb=" N THR G 74 " pdb=" CA THR G 74 " pdb=" C THR G 74 " ideal model delta sigma weight residual 111.28 106.41 4.87 1.09e+00 8.42e-01 2.00e+01 angle pdb=" N GLU B 76 " pdb=" CA GLU B 76 " pdb=" C GLU B 76 " ideal model delta sigma weight residual 110.43 115.76 -5.33 1.31e+00 5.83e-01 1.66e+01 angle pdb=" C ILE F 266 " pdb=" CA ILE F 266 " pdb=" CB ILE F 266 " ideal model delta sigma weight residual 113.70 109.87 3.83 9.50e-01 1.11e+00 1.63e+01 angle pdb=" N TRP B 174 " pdb=" CA TRP B 174 " pdb=" C TRP B 174 " ideal model delta sigma weight residual 111.36 115.66 -4.30 1.09e+00 8.42e-01 1.56e+01 ... (remaining 21016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 8217 17.83 - 35.65: 741 35.65 - 53.48: 179 53.48 - 71.31: 46 71.31 - 89.14: 20 Dihedral angle restraints: 9203 sinusoidal: 4035 harmonic: 5168 Sorted by residual: dihedral pdb=" CA TYR B 110 " pdb=" C TYR B 110 " pdb=" N TYR B 111 " pdb=" CA TYR B 111 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA GLN F 168 " pdb=" C GLN F 168 " pdb=" N ARG F 169 " pdb=" CA ARG F 169 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA TYR G 110 " pdb=" C TYR G 110 " pdb=" N TYR G 111 " pdb=" CA TYR G 111 " ideal model delta harmonic sigma weight residual 180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 9200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1758 0.045 - 0.090: 291 0.090 - 0.135: 121 0.135 - 0.180: 11 0.180 - 0.225: 2 Chirality restraints: 2183 Sorted by residual: chirality pdb=" CA PHE A 206 " pdb=" N PHE A 206 " pdb=" C PHE A 206 " pdb=" CB PHE A 206 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C3' A K 3 " pdb=" C4' A K 3 " pdb=" O3' A K 3 " pdb=" C2' A K 3 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA VAL G 85 " pdb=" N VAL G 85 " pdb=" C VAL G 85 " pdb=" CB VAL G 85 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 2180 not shown) Planarity restraints: 2639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 76 " -0.021 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C GLU B 76 " 0.074 2.00e-02 2.50e+03 pdb=" O GLU B 76 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG B 77 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 103 " 0.012 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C ALA G 103 " -0.039 2.00e-02 2.50e+03 pdb=" O ALA G 103 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP G 104 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 79 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C TRP B 79 " 0.039 2.00e-02 2.50e+03 pdb=" O TRP B 79 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 80 " -0.013 2.00e-02 2.50e+03 ... (remaining 2636 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3437 2.79 - 3.32: 14109 3.32 - 3.85: 23897 3.85 - 4.37: 28511 4.37 - 4.90: 48814 Nonbonded interactions: 118768 Sorted by model distance: nonbonded pdb=" OH TYR E 79 " pdb=" O PRO E 91 " model vdw 2.264 2.440 nonbonded pdb=" OE2 GLU F 191 " pdb=" OH TYR F 222 " model vdw 2.271 2.440 nonbonded pdb=" N GLU E 64 " pdb=" OE1 GLU E 64 " model vdw 2.272 2.520 nonbonded pdb=" OG1 THR I 23 " pdb=" O LYS I 55 " model vdw 2.301 2.440 nonbonded pdb=" OE1 GLN F 57 " pdb=" OH TYR F 59 " model vdw 2.305 2.440 ... (remaining 118763 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' 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' and (resid 2 through 80 or resid 89 through 96)) selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' } 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: 2.620 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: 9.700 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 45.780 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 0.050 15490 Z= 0.239 Angle : 0.573 6.657 21021 Z= 0.334 Chirality : 0.041 0.225 2183 Planarity : 0.005 0.065 2639 Dihedral : 15.035 89.136 5851 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 1728 helix: 1.69 (0.21), residues: 599 sheet: -0.27 (0.28), residues: 336 loop : -0.16 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 113 HIS 0.008 0.001 HIS J 27 PHE 0.013 0.001 PHE A 206 TYR 0.017 0.001 TYR J 79 ARG 0.010 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 time to evaluate : 1.659 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: E 38 THR cc_start: 0.8612 (p) cc_final: 0.8355 (p) REVERT: E 74 CYS cc_start: 0.7224 (m) cc_final: 0.6858 (m) REVERT: E 77 PHE cc_start: 0.8233 (m-10) cc_final: 0.7953 (m-80) REVERT: F 219 TYR cc_start: 0.7259 (m-80) cc_final: 0.7056 (m-10) REVERT: F 285 TRP cc_start: 0.6895 (m100) cc_final: 0.6644 (m100) REVERT: G 1 MET cc_start: 0.6735 (ppp) cc_final: 0.6363 (ppp) REVERT: G 99 ASP cc_start: 0.8225 (t0) cc_final: 0.7817 (t70) REVERT: G 168 LYS cc_start: 0.8654 (tmtt) cc_final: 0.8232 (tptp) REVERT: H 11 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8371 (mmtt) REVERT: H 122 MET cc_start: 0.8513 (mtt) cc_final: 0.7645 (mtm) REVERT: J 105 MET cc_start: 0.4213 (mmt) cc_final: 0.3863 (mmp) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.3383 time to fit residues: 129.0375 Evaluate side-chains 165 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- 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 E 61 ASN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS G 105 GLN H 41 GLN ** 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: 0.7735 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15490 Z= 0.414 Angle : 0.672 7.170 21021 Z= 0.352 Chirality : 0.045 0.171 2183 Planarity : 0.005 0.066 2639 Dihedral : 8.076 59.866 2198 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.52 % Allowed : 9.86 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.48 (0.20), residues: 1728 helix: 1.45 (0.21), residues: 622 sheet: -0.48 (0.27), residues: 357 loop : -0.12 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 89 HIS 0.008 0.001 HIS J 27 PHE 0.019 0.002 PHE C 32 TYR 0.017 0.002 TYR B 135 ARG 0.005 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 1.530 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: B 70 TRP cc_start: 0.7624 (OUTLIER) cc_final: 0.7106 (m-10) REVERT: E 38 THR cc_start: 0.8709 (p) cc_final: 0.8338 (p) REVERT: E 70 LEU cc_start: 0.9098 (tt) cc_final: 0.8752 (tp) REVERT: E 74 CYS cc_start: 0.7435 (m) cc_final: 0.6825 (m) REVERT: E 77 PHE cc_start: 0.8228 (m-80) cc_final: 0.7966 (m-80) REVERT: E 104 LEU cc_start: 0.9090 (tt) cc_final: 0.8852 (tp) REVERT: G 1 MET cc_start: 0.6847 (ppp) cc_final: 0.6328 (ppp) REVERT: G 99 ASP cc_start: 0.7975 (t0) cc_final: 0.7618 (t0) REVERT: G 101 GLU cc_start: 0.8812 (mp0) cc_final: 0.8550 (mp0) REVERT: G 168 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8348 (tptp) REVERT: J 105 MET cc_start: 0.4383 (mmt) cc_final: 0.4026 (mmp) outliers start: 24 outliers final: 14 residues processed: 187 average time/residue: 0.2751 time to fit residues: 76.8837 Evaluate side-chains 171 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 101 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 105 optimal weight: 0.3980 chunk 42 optimal weight: 0.8980 chunk 154 optimal weight: 30.0000 chunk 167 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15490 Z= 0.222 Angle : 0.575 11.218 21021 Z= 0.296 Chirality : 0.041 0.171 2183 Planarity : 0.005 0.062 2639 Dihedral : 7.785 59.397 2198 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.21 % Allowed : 11.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.75 (0.21), residues: 1728 helix: 1.66 (0.22), residues: 620 sheet: -0.33 (0.27), residues: 357 loop : 0.06 (0.23), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 361 HIS 0.009 0.001 HIS B 80 PHE 0.012 0.001 PHE F 206 TYR 0.016 0.001 TYR B 147 ARG 0.007 0.000 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 1.677 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: A 152 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7897 (mtm) REVERT: B 70 TRP cc_start: 0.7565 (OUTLIER) cc_final: 0.7164 (m-10) REVERT: E 38 THR cc_start: 0.8579 (p) cc_final: 0.8233 (p) REVERT: E 70 LEU cc_start: 0.9200 (tt) cc_final: 0.8870 (tt) REVERT: E 74 CYS cc_start: 0.7480 (m) cc_final: 0.6818 (m) REVERT: E 77 PHE cc_start: 0.8341 (m-80) cc_final: 0.7996 (m-80) REVERT: G 1 MET cc_start: 0.6955 (ppp) cc_final: 0.6374 (ppp) REVERT: G 8 MET cc_start: 0.8765 (tpp) cc_final: 0.8547 (tpp) REVERT: G 74 THR cc_start: 0.7271 (OUTLIER) cc_final: 0.7070 (m) REVERT: G 99 ASP cc_start: 0.8036 (t0) cc_final: 0.7665 (t70) REVERT: G 101 GLU cc_start: 0.8850 (mp0) cc_final: 0.8388 (mp0) REVERT: G 168 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8327 (tptp) REVERT: H 64 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6601 (tp) REVERT: J 105 MET cc_start: 0.4360 (mmt) cc_final: 0.4022 (mmp) outliers start: 35 outliers final: 21 residues processed: 181 average time/residue: 0.2664 time to fit residues: 72.4971 Evaluate side-chains 178 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 85 VAL Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 44 optimal weight: 6.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS B 12 GLN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 15490 Z= 0.438 Angle : 0.653 12.177 21021 Z= 0.341 Chirality : 0.044 0.179 2183 Planarity : 0.005 0.052 2639 Dihedral : 7.986 59.459 2198 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.59 % Allowed : 13.59 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.37 (0.20), residues: 1728 helix: 1.25 (0.21), residues: 626 sheet: -0.53 (0.26), residues: 358 loop : -0.08 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 94 HIS 0.009 0.001 HIS G 48 PHE 0.014 0.002 PHE G 112 TYR 0.020 0.002 TYR B 147 ARG 0.006 0.001 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 164 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7917 (mtm) REVERT: B 70 TRP cc_start: 0.7524 (OUTLIER) cc_final: 0.7083 (m-10) REVERT: E 38 THR cc_start: 0.8687 (p) cc_final: 0.8477 (p) REVERT: E 70 LEU cc_start: 0.9209 (tt) cc_final: 0.8934 (tt) REVERT: E 74 CYS cc_start: 0.7401 (m) cc_final: 0.7086 (m) REVERT: E 77 PHE cc_start: 0.8360 (m-80) cc_final: 0.8058 (m-80) REVERT: E 104 LEU cc_start: 0.9045 (tp) cc_final: 0.8728 (mt) REVERT: G 1 MET cc_start: 0.7133 (ppp) cc_final: 0.6462 (ppp) REVERT: G 168 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8324 (tptp) REVERT: H 98 LYS cc_start: 0.9160 (tttt) cc_final: 0.8921 (ttmt) REVERT: H 122 MET cc_start: 0.8213 (mmm) cc_final: 0.7704 (mmm) REVERT: J 105 MET cc_start: 0.4459 (mmt) cc_final: 0.4112 (mmp) outliers start: 41 outliers final: 31 residues processed: 191 average time/residue: 0.2822 time to fit residues: 79.3665 Evaluate side-chains 187 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 370 ASP Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 16 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 0.0470 chunk 67 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 3 ASN C 67 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 HIS ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15490 Z= 0.159 Angle : 0.556 9.967 21021 Z= 0.285 Chirality : 0.040 0.175 2183 Planarity : 0.004 0.051 2639 Dihedral : 7.573 59.138 2198 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.21 % Allowed : 15.04 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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 (0.21), residues: 1728 helix: 1.62 (0.21), residues: 632 sheet: -0.29 (0.27), residues: 357 loop : 0.03 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 361 HIS 0.005 0.001 HIS B 108 PHE 0.011 0.001 PHE F 54 TYR 0.013 0.001 TYR F 22 ARG 0.014 0.000 ARG A 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7879 (mtm) REVERT: A 227 MET cc_start: 0.7042 (mmm) cc_final: 0.6568 (mmm) REVERT: A 268 PHE cc_start: 0.7566 (OUTLIER) cc_final: 0.7097 (t80) REVERT: B 70 TRP cc_start: 0.7517 (OUTLIER) cc_final: 0.7141 (m-10) REVERT: E 38 THR cc_start: 0.8603 (p) cc_final: 0.8389 (p) REVERT: E 77 PHE cc_start: 0.8350 (m-80) cc_final: 0.8064 (m-80) REVERT: E 104 LEU cc_start: 0.8992 (tp) cc_final: 0.8658 (mt) REVERT: G 1 MET cc_start: 0.6960 (ppp) cc_final: 0.6316 (ppp) REVERT: G 74 THR cc_start: 0.7303 (p) cc_final: 0.7091 (m) REVERT: G 168 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8300 (tptp) REVERT: H 122 MET cc_start: 0.8123 (mmm) cc_final: 0.7609 (mmm) REVERT: I 7 ILE cc_start: 0.5031 (OUTLIER) cc_final: 0.4539 (mm) REVERT: I 13 THR cc_start: 0.7730 (m) cc_final: 0.7270 (p) REVERT: J 105 MET cc_start: 0.4490 (mmt) cc_final: 0.4157 (mmp) outliers start: 35 outliers final: 23 residues processed: 190 average time/residue: 0.2588 time to fit residues: 74.4083 Evaluate side-chains 177 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain E residue 99 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 7 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 7.9990 chunk 147 optimal weight: 30.0000 chunk 32 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 54 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15490 Z= 0.225 Angle : 0.556 9.138 21021 Z= 0.285 Chirality : 0.040 0.200 2183 Planarity : 0.004 0.051 2639 Dihedral : 7.584 59.152 2198 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.09 % Allowed : 15.74 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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 (0.21), residues: 1728 helix: 1.63 (0.21), residues: 630 sheet: -0.41 (0.26), residues: 364 loop : 0.01 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP G 70 HIS 0.008 0.001 HIS G 56 PHE 0.013 0.001 PHE D 15 TYR 0.011 0.001 TYR F 22 ARG 0.011 0.000 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.811 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: A 152 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7867 (mtm) REVERT: A 227 MET cc_start: 0.7292 (mmm) cc_final: 0.6629 (mmm) REVERT: A 268 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7194 (t80) REVERT: B 70 TRP cc_start: 0.7520 (OUTLIER) cc_final: 0.7126 (m-10) REVERT: E 38 THR cc_start: 0.8668 (p) cc_final: 0.8463 (p) REVERT: E 77 PHE cc_start: 0.8383 (m-80) cc_final: 0.8067 (m-80) REVERT: E 104 LEU cc_start: 0.9012 (tp) cc_final: 0.8660 (mt) REVERT: G 1 MET cc_start: 0.6978 (ppp) cc_final: 0.6331 (ppp) REVERT: G 168 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8298 (tptp) REVERT: H 122 MET cc_start: 0.8142 (mmm) cc_final: 0.7873 (mmm) REVERT: I 7 ILE cc_start: 0.4911 (OUTLIER) cc_final: 0.4330 (mm) REVERT: I 13 THR cc_start: 0.7600 (m) cc_final: 0.7183 (p) REVERT: J 77 PHE cc_start: 0.5946 (m-80) cc_final: 0.5721 (m-80) REVERT: J 105 MET cc_start: 0.4452 (mmt) cc_final: 0.4104 (mmp) outliers start: 33 outliers final: 24 residues processed: 173 average time/residue: 0.2567 time to fit residues: 67.6360 Evaluate side-chains 178 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain G residue 34 LYS Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 101 MET Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 138 optimal weight: 0.1980 chunk 91 optimal weight: 0.6980 chunk 163 optimal weight: 30.0000 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15490 Z= 0.176 Angle : 0.543 10.941 21021 Z= 0.277 Chirality : 0.040 0.180 2183 Planarity : 0.004 0.050 2639 Dihedral : 7.492 59.036 2198 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.28 % Allowed : 16.12 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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 (0.21), residues: 1728 helix: 1.70 (0.21), residues: 630 sheet: -0.24 (0.25), residues: 395 loop : 0.08 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP F 361 HIS 0.007 0.001 HIS G 48 PHE 0.016 0.001 PHE I 15 TYR 0.019 0.001 TYR B 147 ARG 0.011 0.000 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 1.791 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: A 152 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7834 (mtm) REVERT: A 227 MET cc_start: 0.7317 (mmm) cc_final: 0.6853 (mmm) REVERT: A 268 PHE cc_start: 0.7576 (OUTLIER) cc_final: 0.7186 (t80) REVERT: B 70 TRP cc_start: 0.7497 (OUTLIER) cc_final: 0.7151 (m-10) REVERT: E 38 THR cc_start: 0.8630 (p) cc_final: 0.8418 (p) REVERT: E 77 PHE cc_start: 0.8368 (m-80) cc_final: 0.8049 (m-80) REVERT: E 104 LEU cc_start: 0.8998 (tp) cc_final: 0.8641 (mt) REVERT: G 1 MET cc_start: 0.6976 (ppp) cc_final: 0.6324 (ppp) REVERT: G 64 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8564 (tt) REVERT: G 168 LYS cc_start: 0.8729 (tmtt) cc_final: 0.8309 (tptp) REVERT: H 122 MET cc_start: 0.8133 (mmm) cc_final: 0.7915 (mmm) REVERT: I 7 ILE cc_start: 0.4752 (OUTLIER) cc_final: 0.4393 (mm) REVERT: J 77 PHE cc_start: 0.5953 (m-80) cc_final: 0.5729 (m-80) REVERT: J 105 MET cc_start: 0.4510 (mmt) cc_final: 0.4179 (mmp) outliers start: 36 outliers final: 25 residues processed: 182 average time/residue: 0.2437 time to fit residues: 67.7235 Evaluate side-chains 173 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 111 optimal weight: 0.0570 chunk 81 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15490 Z= 0.167 Angle : 0.565 14.548 21021 Z= 0.284 Chirality : 0.040 0.179 2183 Planarity : 0.004 0.048 2639 Dihedral : 7.462 59.014 2198 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.28 % Allowed : 16.56 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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 (0.21), residues: 1728 helix: 1.68 (0.21), residues: 632 sheet: -0.19 (0.27), residues: 355 loop : 0.06 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 361 HIS 0.005 0.001 HIS G 48 PHE 0.013 0.001 PHE I 15 TYR 0.015 0.001 TYR B 147 ARG 0.011 0.000 ARG D 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.907 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: A 152 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7822 (mtm) REVERT: A 268 PHE cc_start: 0.7554 (OUTLIER) cc_final: 0.7164 (t80) REVERT: B 70 TRP cc_start: 0.7416 (OUTLIER) cc_final: 0.7116 (m-10) REVERT: D 44 LEU cc_start: 0.8603 (mp) cc_final: 0.8222 (mt) REVERT: E 77 PHE cc_start: 0.8378 (m-10) cc_final: 0.8043 (m-80) REVERT: E 104 LEU cc_start: 0.9021 (tp) cc_final: 0.8630 (mt) REVERT: G 1 MET cc_start: 0.6923 (ppp) cc_final: 0.6288 (ppp) REVERT: G 64 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8569 (tt) REVERT: G 168 LYS cc_start: 0.8744 (tmtt) cc_final: 0.8323 (tptp) REVERT: H 122 MET cc_start: 0.8129 (mmm) cc_final: 0.7919 (mmm) REVERT: I 7 ILE cc_start: 0.4623 (OUTLIER) cc_final: 0.4095 (mm) REVERT: J 77 PHE cc_start: 0.5932 (m-80) cc_final: 0.5675 (m-80) REVERT: J 105 MET cc_start: 0.4497 (mmt) cc_final: 0.4169 (mmp) outliers start: 36 outliers final: 28 residues processed: 176 average time/residue: 0.2463 time to fit residues: 66.9491 Evaluate side-chains 179 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 146 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 268 PHE Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 80 HIS Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 97 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 152 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 144 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 161 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 127 HIS C 67 GLN ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 15490 Z= 0.544 Angle : 0.731 13.637 21021 Z= 0.377 Chirality : 0.046 0.183 2183 Planarity : 0.005 0.053 2639 Dihedral : 7.982 59.103 2198 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.72 % Allowed : 16.37 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.27 (0.20), residues: 1728 helix: 1.17 (0.21), residues: 628 sheet: -0.54 (0.26), residues: 359 loop : -0.18 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP F 361 HIS 0.008 0.001 HIS F 304 PHE 0.026 0.002 PHE J 29 TYR 0.021 0.002 TYR B 111 ARG 0.010 0.001 ARG F 320 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 145 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7973 (mtm) REVERT: A 318 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: B 70 TRP cc_start: 0.7577 (OUTLIER) cc_final: 0.7257 (m-10) REVERT: D 44 LEU cc_start: 0.8731 (mp) cc_final: 0.8368 (mt) REVERT: E 77 PHE cc_start: 0.8380 (m-80) cc_final: 0.8006 (m-80) REVERT: E 92 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8136 (tm-30) REVERT: E 104 LEU cc_start: 0.9067 (tp) cc_final: 0.8680 (mt) REVERT: G 1 MET cc_start: 0.7184 (ppp) cc_final: 0.6490 (ppp) REVERT: G 64 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8754 (tt) REVERT: H 98 LYS cc_start: 0.9179 (tttt) cc_final: 0.8938 (ttmt) REVERT: I 7 ILE cc_start: 0.4176 (OUTLIER) cc_final: 0.3764 (mm) REVERT: J 105 MET cc_start: 0.4530 (mmt) cc_final: 0.4184 (mmp) outliers start: 43 outliers final: 32 residues processed: 176 average time/residue: 0.2495 time to fit residues: 67.2066 Evaluate side-chains 176 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 139 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 34 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 52 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.0770 chunk 76 optimal weight: 0.1980 chunk 112 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 GLN C 67 GLN C 134 GLN ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15490 Z= 0.171 Angle : 0.613 14.048 21021 Z= 0.308 Chirality : 0.041 0.183 2183 Planarity : 0.004 0.047 2639 Dihedral : 7.615 58.920 2198 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.02 % Allowed : 17.26 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % 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: 0.62 (0.20), residues: 1728 helix: 1.52 (0.21), residues: 633 sheet: -0.31 (0.27), residues: 361 loop : -0.07 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 70 HIS 0.005 0.001 HIS B 108 PHE 0.040 0.001 PHE J 77 TYR 0.016 0.001 TYR B 147 ARG 0.020 0.000 ARG C 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3456 Ramachandran restraints generated. 1728 Oldfield, 0 Emsley, 1728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 150 time to evaluate : 1.703 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: A 152 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7829 (mtm) REVERT: B 70 TRP cc_start: 0.7531 (OUTLIER) cc_final: 0.7165 (m-10) REVERT: D 44 LEU cc_start: 0.8689 (mp) cc_final: 0.8315 (mt) REVERT: E 77 PHE cc_start: 0.8422 (m-10) cc_final: 0.8050 (m-80) REVERT: E 104 LEU cc_start: 0.9000 (tp) cc_final: 0.8609 (mt) REVERT: G 1 MET cc_start: 0.7129 (ppp) cc_final: 0.6455 (ppp) REVERT: G 64 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8675 (tt) REVERT: G 168 LYS cc_start: 0.8818 (tmtt) cc_final: 0.8536 (tptp) REVERT: I 6 MET cc_start: 0.3271 (mmm) cc_final: 0.2661 (tpt) REVERT: I 7 ILE cc_start: 0.4365 (OUTLIER) cc_final: 0.3887 (mm) REVERT: J 105 MET cc_start: 0.4433 (mmt) cc_final: 0.4094 (mmp) outliers start: 32 outliers final: 24 residues processed: 172 average time/residue: 0.2365 time to fit residues: 63.7047 Evaluate side-chains 174 residues out of total 1582 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain B residue 70 TRP Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain E residue 63 ARG Chi-restraints excluded: chain E residue 79 TYR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 90 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 361 TRP Chi-restraints excluded: chain G residue 23 SER Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 78 ASP Chi-restraints excluded: chain H residue 17 PHE Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 50 ASP Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 138 LEU Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 19 optimal weight: 0.0670 chunk 37 optimal weight: 0.3980 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 138 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN ** J 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.098381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.068230 restraints weight = 59057.844| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 4.99 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15490 Z= 0.163 Angle : 0.601 14.812 21021 Z= 0.299 Chirality : 0.040 0.179 2183 Planarity : 0.004 0.045 2639 Dihedral : 7.529 58.921 2198 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.58 % Allowed : 18.02 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.20), residues: 1728 helix: 1.55 (0.21), residues: 633 sheet: -0.17 (0.27), residues: 357 loop : -0.09 (0.23), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 70 HIS 0.010 0.001 HIS G 48 PHE 0.017 0.001 PHE G 39 TYR 0.020 0.001 TYR B 147 ARG 0.010 0.000 ARG F 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3201.80 seconds wall clock time: 59 minutes 30.39 seconds (3570.39 seconds total)