Starting phenix.real_space_refine on Mon Mar 18 18:46:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdy_24427/03_2024/7rdy_24427_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdy_24427/03_2024/7rdy_24427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdy_24427/03_2024/7rdy_24427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdy_24427/03_2024/7rdy_24427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdy_24427/03_2024/7rdy_24427_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rdy_24427/03_2024/7rdy_24427_updated.pdb" } resolution = 3.1 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= 0.012 sd= 1.106 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 84 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13561 2.51 5 N 3680 2.21 5 O 4351 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 36": "OD1" <-> "OD2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A PHE 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A ASP 711": "OD1" <-> "OD2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A PHE 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 52": "OD1" <-> "OD2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "B TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21846 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1415 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 178} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4570 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4557 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 558} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "P" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 719 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 15, 'rna3p_pyr': 18} Link IDs: {'rna3p': 33} Chain: "T" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 934 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 21, 'rna3p_pyr': 19} Link IDs: {'rna2p': 4, 'rna3p': 39} Chain breaks: 1 Chain: "A" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 127 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 3, 'ADP': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 62.106 45.789 115.707 1.00 41.22 S ATOM 2495 SG CYS A 306 62.060 46.963 119.484 1.00 37.19 S ATOM 2527 SG CYS A 310 63.654 43.696 118.430 1.00 32.94 S ATOM 3935 SG CYS A 487 64.686 61.094 102.015 1.00 43.02 S ATOM 5188 SG CYS A 645 63.591 62.902 105.190 1.00 50.04 S ATOM 5194 SG CYS A 646 62.677 59.303 104.524 1.00 47.24 S ATOM 10896 SG CYS E 5 113.227 64.615 52.394 1.00 74.74 S ATOM 10917 SG CYS E 8 116.514 64.781 53.678 1.00 79.45 S ATOM 11055 SG CYS E 26 114.610 68.068 53.500 1.00 77.30 S ATOM 11076 SG CYS E 29 115.928 66.820 50.476 1.00 81.66 S ATOM 11241 SG CYS E 50 93.963 82.419 48.935 1.00 92.08 S ATOM 11271 SG CYS E 55 92.816 82.744 45.208 1.00101.11 S ATOM 11404 SG CYS E 72 95.446 85.167 46.649 1.00 94.15 S ATOM 10978 SG CYS E 16 105.749 67.409 45.042 1.00 76.77 S ATOM 10993 SG CYS E 19 106.018 64.069 43.240 1.00 80.95 S ATOM 15466 SG CYS F 5 61.179 64.236 54.799 1.00111.78 S ATOM 15487 SG CYS F 8 64.099 64.826 52.749 1.00115.39 S ATOM 15625 SG CYS F 26 63.355 67.628 54.682 1.00114.39 S ATOM 15646 SG CYS F 29 60.950 67.399 52.404 1.00118.98 S ATOM 15811 SG CYS F 50 54.005 80.679 74.901 1.00127.65 S ATOM 15841 SG CYS F 55 50.269 81.168 74.675 1.00134.09 S ATOM 15974 SG CYS F 72 52.344 83.796 73.213 1.00132.86 S ATOM 15548 SG CYS F 16 51.755 67.264 60.933 1.00113.89 S ATOM 15563 SG CYS F 19 50.479 64.123 59.031 1.00123.51 S Time building chain proxies: 12.19, per 1000 atoms: 0.56 Number of scatterers: 21846 At special positions: 0 Unit cell: (145.52, 150.87, 178.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 84 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4351 8.00 N 3680 7.00 C 13561 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: 8.82 Conformation dependent library (CDL) restraints added in 3.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 8 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 26 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 5 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 29 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 72 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 55 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 50 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E1002 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 19 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 26 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 20 sheets defined 36.5% alpha, 9.9% beta 34 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 9.21 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 140 through 148 removed outlier: 4.055A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 169 through 197 removed outlier: 3.723A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N CYS A 193 " --> pdb=" O VAL A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 209 No H-bonds generated for 'chain 'A' and resid 207 through 209' Processing helix chain 'A' and resid 235 through 238 No H-bonds generated for 'chain 'A' and resid 235 through 238' Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.558A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 247 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.802A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.759A pdb=" N ASP A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.316A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 512 through 518 Processing helix chain 'A' and resid 521 through 531 Processing helix chain 'A' and resid 562 through 579 removed outlier: 4.179A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 688 through 708 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 847 through 850 Processing helix chain 'A' and resid 857 through 865 Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 875 through 901 removed outlier: 4.513A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 918 through 924 removed outlier: 4.186A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 32 through 96 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 141 Processing helix chain 'C' and resid 3 through 19 removed outlier: 4.304A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.645A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.744A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 71 No H-bonds generated for 'chain 'C' and resid 68 through 71' Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 33 through 81 Processing helix chain 'D' and resid 84 through 98 Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.952A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.642A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 102 through 104 No H-bonds generated for 'chain 'E' and resid 102 through 104' Processing helix chain 'E' and resid 106 through 111 Processing helix chain 'E' and resid 118 through 122 Processing helix chain 'E' and resid 128 through 148 removed outlier: 3.838A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 274 Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.540A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 381 through 390 Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 424 through 431 Processing helix chain 'E' and resid 446 through 452 Processing helix chain 'E' and resid 490 through 501 removed outlier: 3.638A pdb=" N THR E 501 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 508 removed outlier: 4.176A pdb=" N LYS E 508 " --> pdb=" O ALA E 505 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 521 Processing helix chain 'E' and resid 534 through 536 No H-bonds generated for 'chain 'E' and resid 534 through 536' Processing helix chain 'E' and resid 558 through 567 removed outlier: 4.639A pdb=" N ARG E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 584 Processing helix chain 'F' and resid 27 through 36 Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 117 through 122 Processing helix chain 'F' and resid 128 through 147 Processing helix chain 'F' and resid 263 through 274 removed outlier: 3.568A pdb=" N VAL F 266 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA F 267 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET F 274 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 Processing helix chain 'F' and resid 311 through 323 Processing helix chain 'F' and resid 376 through 378 No H-bonds generated for 'chain 'F' and resid 376 through 378' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 429 Processing helix chain 'F' and resid 446 through 455 Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'F' and resid 516 through 525 removed outlier: 3.533A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 567 removed outlier: 3.722A pdb=" N ARG F 567 " --> pdb=" O VAL F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 583 Processing sheet with id= A, first strand: chain 'A' and resid 18 through 21 removed outlier: 4.382A pdb=" N ARG A 18 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 56 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= D, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= E, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.445A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 800 through 802 removed outlier: 4.391A pdb=" N SER A 754 " --> pdb=" O CYS A 765 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= H, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.445A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.210A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 69 through 71 Processing sheet with id= K, first strand: chain 'E' and resid 181 through 183 Processing sheet with id= L, first strand: chain 'E' and resid 277 through 280 removed outlier: 6.365A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 305 " --> pdb=" O ILE E 370 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 471 through 475 removed outlier: 5.980A pdb=" N ILE E 572 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N MET E 474 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N CYS E 574 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER E 513 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 152 through 157 removed outlier: 7.260A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= P, first strand: chain 'F' and resid 152 through 154 Processing sheet with id= Q, first strand: chain 'F' and resid 224 through 226 removed outlier: 4.067A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 277 through 281 removed outlier: 6.962A pdb=" N TYR F 396 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N LEU F 280 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TYR F 398 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL F 305 " --> pdb=" O ILE F 370 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 366 through 368 Processing sheet with id= T, first strand: chain 'F' and resid 510 through 513 removed outlier: 6.740A pdb=" N GLY F 571 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE F 546 " --> pdb=" O GLY F 571 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU F 573 " --> pdb=" O PHE F 546 " (cutoff:3.500A) 689 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 7.48 Time building geometry restraints manager: 9.54 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: 4558 1.32 - 1.45: 5643 1.45 - 1.57: 11836 1.57 - 1.69: 218 1.69 - 1.81: 220 Bond restraints: 22475 Sorted by residual: bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" F3 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.52e+01 bond pdb=" F3 AF3 E1005 " pdb="AL AF3 E1005 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.794 -0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" F1 AF3 E1005 " pdb="AL AF3 E1005 " ideal model delta sigma weight residual 1.637 1.791 -0.154 2.00e-02 2.50e+03 5.96e+01 ... (remaining 22470 not shown) Histogram of bond angle deviations from ideal: 92.77 - 101.85: 177 101.85 - 110.92: 8908 110.92 - 120.00: 12232 120.00 - 129.08: 9435 129.08 - 138.16: 180 Bond angle restraints: 30932 Sorted by residual: angle pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta sigma weight residual 121.70 138.16 -16.46 1.80e+00 3.09e-01 8.36e+01 angle pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta sigma weight residual 121.70 135.43 -13.73 1.80e+00 3.09e-01 5.82e+01 angle pdb=" C SER F 80 " pdb=" N PHE F 81 " pdb=" CA PHE F 81 " ideal model delta sigma weight residual 121.70 131.57 -9.87 1.80e+00 3.09e-01 3.01e+01 angle pdb=" O3' C P 24 " pdb=" C3' C P 24 " pdb=" C2' C P 24 " ideal model delta sigma weight residual 113.70 120.53 -6.83 1.50e+00 4.44e-01 2.07e+01 angle pdb=" N ALA E 454 " pdb=" CA ALA E 454 " pdb=" C ALA E 454 " ideal model delta sigma weight residual 114.56 108.81 5.75 1.27e+00 6.20e-01 2.05e+01 ... (remaining 30927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 13085 35.18 - 70.37: 536 70.37 - 105.55: 71 105.55 - 140.73: 13 140.73 - 175.91: 4 Dihedral angle restraints: 13709 sinusoidal: 6151 harmonic: 7558 Sorted by residual: dihedral pdb=" CA SER D 31 " pdb=" C SER D 31 " pdb=" N GLU D 32 " pdb=" CA GLU D 32 " ideal model delta harmonic sigma weight residual -180.00 -49.12 -130.88 0 5.00e+00 4.00e-02 6.85e+02 dihedral pdb=" CA ASN F 190 " pdb=" C ASN F 190 " pdb=" N SER F 191 " pdb=" CA SER F 191 " ideal model delta harmonic sigma weight residual 180.00 140.29 39.71 0 5.00e+00 4.00e-02 6.31e+01 dihedral pdb=" CA LYS F 189 " pdb=" C LYS F 189 " pdb=" N ASN F 190 " pdb=" CA ASN F 190 " ideal model delta harmonic sigma weight residual 0.00 38.22 -38.22 0 5.00e+00 4.00e-02 5.84e+01 ... (remaining 13706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.041: 3602 1.041 - 2.081: 0 2.081 - 3.122: 0 3.122 - 4.163: 0 4.163 - 5.203: 2 Chirality restraints: 3604 Sorted by residual: chirality pdb=" C6 1N7 A1005 " pdb=" C18 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C7 1N7 A1005 " both_signs ideal model delta sigma weight residual False -2.43 2.77 -5.20 2.00e-01 2.50e+01 6.77e+02 chirality pdb=" C18 1N7 A1005 " pdb=" C17 1N7 A1005 " pdb=" C19 1N7 A1005 " pdb=" C6 1N7 A1005 " both_signs ideal model delta sigma weight residual False 2.53 -2.63 5.17 2.00e-01 2.50e+01 6.67e+02 chirality pdb=" C17 1N7 A1006 " pdb=" C16 1N7 A1006 " pdb=" C18 1N7 A1006 " pdb=" O3 1N7 A1006 " both_signs ideal model delta sigma weight residual False 2.40 2.83 -0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 3601 not shown) Planarity restraints: 3630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 490 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO F 491 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 491 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 491 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 407 " -0.051 5.00e-02 4.00e+02 7.81e-02 9.75e+00 pdb=" N PRO E 408 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO E 408 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 408 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS F 444 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO F 445 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 445 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 445 " -0.041 5.00e-02 4.00e+02 ... (remaining 3627 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 195 2.50 - 3.10: 15524 3.10 - 3.70: 34677 3.70 - 4.30: 49321 4.30 - 4.90: 81134 Nonbonded interactions: 180851 Sorted by model distance: nonbonded pdb=" N SER F 289 " pdb="MG MG F1004 " model vdw 1.894 2.250 nonbonded pdb=" OG SER E 289 " pdb="MG MG E1004 " model vdw 1.980 2.170 nonbonded pdb=" OG SER F 289 " pdb="MG MG F1004 " model vdw 2.019 2.170 nonbonded pdb="MG MG A1003 " pdb=" O1B ADP A1004 " model vdw 2.053 2.170 nonbonded pdb=" O3B ADP E1003 " pdb="MG MG E1004 " model vdw 2.063 2.170 ... (remaining 180846 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 'B' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 474 or (resid 475 through 476 and (name N or nam \ e CA or name C or name O or name CB )) or resid 477 through 590 or resid 1000 th \ rough 1005)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.020 Extract box with map and model: 8.220 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 66.270 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.015 0.163 22475 Z= 0.984 Angle : 1.038 16.463 30932 Z= 0.555 Chirality : 0.138 5.203 3604 Planarity : 0.006 0.080 3630 Dihedral : 18.955 175.913 8835 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 10.18 % Allowed : 12.14 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -2.87 (0.15), residues: 2541 helix: -1.74 (0.14), residues: 1037 sheet: -1.25 (0.28), residues: 328 loop : -2.18 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 916 HIS 0.011 0.002 HIS A 309 PHE 0.029 0.003 PHE B 147 TYR 0.031 0.003 TYR A 788 ARG 0.006 0.001 ARG A 583 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 209 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8188 (t80) cc_final: 0.7925 (t80) REVERT: A 388 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8521 (tp) REVERT: A 477 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7878 (t70) REVERT: A 723 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8151 (tt) REVERT: A 815 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.7616 (mm-40) REVERT: A 891 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 911 ASN cc_start: 0.7810 (t0) cc_final: 0.6718 (t0) REVERT: B 62 MET cc_start: 0.8121 (tmm) cc_final: 0.7733 (tmm) REVERT: B 65 GLN cc_start: 0.8328 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 174 MET cc_start: 0.8307 (tpp) cc_final: 0.8104 (tpt) REVERT: C 69 ASN cc_start: 0.7905 (t0) cc_final: 0.7656 (t0) REVERT: D 12 TYR cc_start: 0.7070 (t80) cc_final: 0.6739 (t80) REVERT: D 32 GLU cc_start: 0.6369 (mm-30) cc_final: 0.6088 (mm-30) REVERT: D 55 MET cc_start: 0.8576 (tpp) cc_final: 0.8311 (tpp) REVERT: D 80 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8053 (mtm-85) REVERT: D 185 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8149 (mt) REVERT: E 105 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7992 (t0) REVERT: E 122 LEU cc_start: 0.8922 (tp) cc_final: 0.8421 (tp) REVERT: E 197 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: E 227 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8084 (tt) REVERT: E 320 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8039 (mtmt) REVERT: E 411 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8699 (mm) REVERT: E 510 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8300 (p) REVERT: E 562 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.8090 (t0) REVERT: F 95 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7702 (p0) REVERT: F 107 ASN cc_start: 0.6940 (OUTLIER) cc_final: 0.6682 (t0) REVERT: F 304 ILE cc_start: 0.5950 (OUTLIER) cc_final: 0.5748 (mp) REVERT: F 576 MET cc_start: 0.2636 (mmm) cc_final: 0.2288 (mmt) REVERT: F 590 LEU cc_start: -0.0578 (OUTLIER) cc_final: -0.0959 (mt) outliers start: 224 outliers final: 112 residues processed: 417 average time/residue: 0.3209 time to fit residues: 206.7196 Evaluate side-chains 285 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 156 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 573 GLN Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 197 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 278 SER Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 449 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 510 VAL Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 107 ASN Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 304 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain F residue 590 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.9990 chunk 197 optimal weight: 0.3980 chunk 109 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 203 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 123 optimal weight: 0.9990 chunk 151 optimal weight: 0.9990 chunk 236 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN A 573 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 HIS F 257 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22475 Z= 0.162 Angle : 0.588 13.842 30932 Z= 0.296 Chirality : 0.040 0.307 3604 Planarity : 0.004 0.066 3630 Dihedral : 16.135 174.400 4443 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.23 % Allowed : 16.91 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.75 (0.16), residues: 2541 helix: -0.40 (0.16), residues: 1030 sheet: -1.21 (0.28), residues: 334 loop : -1.80 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.021 0.001 PHE A 652 TYR 0.014 0.001 TYR B 138 ARG 0.009 0.000 ARG F 567 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 171 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.8222 (tp40) cc_final: 0.7992 (tp-100) REVERT: A 105 ARG cc_start: 0.7858 (tpp80) cc_final: 0.7323 (tpp80) REVERT: B 62 MET cc_start: 0.8112 (tmm) cc_final: 0.7842 (tmm) REVERT: B 69 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 171 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8344 (mm-30) REVERT: B 174 MET cc_start: 0.8319 (tpp) cc_final: 0.8109 (tpt) REVERT: C 34 GLN cc_start: 0.8054 (tp40) cc_final: 0.7716 (tp40) REVERT: C 69 ASN cc_start: 0.7782 (t0) cc_final: 0.7565 (t0) REVERT: D 80 ARG cc_start: 0.8160 (mtm-85) cc_final: 0.7825 (mtm-85) REVERT: E 122 LEU cc_start: 0.8901 (tp) cc_final: 0.8354 (tt) REVERT: E 227 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8164 (tt) REVERT: E 260 ASP cc_start: 0.8280 (p0) cc_final: 0.8033 (t0) REVERT: E 562 ASN cc_start: 0.7914 (OUTLIER) cc_final: 0.7657 (t0) REVERT: F 274 MET cc_start: 0.8356 (mmp) cc_final: 0.8144 (mmp) REVERT: F 531 GLN cc_start: 0.6843 (pp30) cc_final: 0.6220 (mt0) REVERT: F 576 MET cc_start: 0.2458 (mmm) cc_final: 0.2201 (mmt) outliers start: 115 outliers final: 71 residues processed: 280 average time/residue: 0.3443 time to fit residues: 149.2507 Evaluate side-chains 227 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 154 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 480 ILE Chi-restraints excluded: chain E residue 481 THR Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN B 158 GLN E 51 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 HIS ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 HIS ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 ASN F 245 HIS ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 HIS F 349 ASN F 404 GLN F 470 GLN F 492 GLN F 503 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.110 22475 Z= 0.705 Angle : 0.787 13.951 30932 Z= 0.402 Chirality : 0.050 0.319 3604 Planarity : 0.005 0.066 3630 Dihedral : 15.699 170.791 4320 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 6.55 % Allowed : 17.23 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.92 (0.16), residues: 2541 helix: -0.50 (0.16), residues: 1040 sheet: -1.11 (0.29), residues: 318 loop : -2.01 (0.17), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 114 HIS 0.008 0.001 HIS A 572 PHE 0.021 0.003 PHE E 587 TYR 0.027 0.002 TYR A 788 ARG 0.007 0.001 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 154 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7853 (ptmm) REVERT: A 555 ARG cc_start: 0.7250 (ttp-110) cc_final: 0.6949 (ttp-110) REVERT: A 857 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: A 911 ASN cc_start: 0.7693 (t0) cc_final: 0.6564 (t0) REVERT: B 62 MET cc_start: 0.8538 (tmm) cc_final: 0.8319 (tmm) REVERT: B 69 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8224 (tm-30) REVERT: B 70 MET cc_start: 0.7875 (ttm) cc_final: 0.7581 (mtt) REVERT: B 171 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8378 (mm-30) REVERT: C 69 ASN cc_start: 0.7991 (t0) cc_final: 0.7736 (t0) REVERT: D 80 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7955 (mtm-85) REVERT: D 99 ASP cc_start: 0.8276 (t0) cc_final: 0.7975 (t0) REVERT: E 227 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8177 (tt) REVERT: E 262 PHE cc_start: 0.9056 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: E 474 MET cc_start: 0.6306 (ppp) cc_final: 0.6011 (ppp) REVERT: E 562 ASN cc_start: 0.8362 (OUTLIER) cc_final: 0.7987 (t0) REVERT: E 567 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7766 (mmp80) REVERT: F 95 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7920 (p0) REVERT: F 474 MET cc_start: 0.0532 (OUTLIER) cc_final: 0.0137 (mmm) REVERT: F 498 GLU cc_start: 0.5462 (OUTLIER) cc_final: 0.4559 (pt0) outliers start: 144 outliers final: 95 residues processed: 284 average time/residue: 0.3417 time to fit residues: 149.4395 Evaluate side-chains 250 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 146 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 567 ARG Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 411 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Chi-restraints excluded: chain F residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 chunk 251 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 224 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN F 562 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22475 Z= 0.198 Angle : 0.583 13.972 30932 Z= 0.293 Chirality : 0.041 0.359 3604 Planarity : 0.004 0.063 3630 Dihedral : 15.140 172.102 4308 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.64 % Allowed : 19.36 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.44 (0.16), residues: 2541 helix: 0.03 (0.16), residues: 1035 sheet: -1.05 (0.29), residues: 327 loop : -1.81 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.019 0.001 PHE A 652 TYR 0.011 0.001 TYR A 884 ARG 0.004 0.000 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 155 time to evaluate : 2.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7822 (ptmm) REVERT: A 450 ILE cc_start: 0.8647 (tp) cc_final: 0.8305 (tp) REVERT: B 62 MET cc_start: 0.8566 (tmm) cc_final: 0.8359 (tmm) REVERT: B 69 GLN cc_start: 0.8709 (tm-30) cc_final: 0.8192 (tm-30) REVERT: B 70 MET cc_start: 0.7809 (ttm) cc_final: 0.7532 (mtt) REVERT: C 34 GLN cc_start: 0.8064 (tp40) cc_final: 0.7742 (tp40) REVERT: C 38 ASP cc_start: 0.7311 (m-30) cc_final: 0.6338 (m-30) REVERT: C 69 ASN cc_start: 0.7893 (t0) cc_final: 0.7665 (t0) REVERT: D 80 ARG cc_start: 0.8216 (mtm-85) cc_final: 0.7868 (mtm-85) REVERT: D 99 ASP cc_start: 0.8223 (t0) cc_final: 0.7994 (t0) REVERT: D 157 GLN cc_start: 0.8275 (mm110) cc_final: 0.8003 (mm110) REVERT: E 163 LEU cc_start: 0.9127 (mt) cc_final: 0.8716 (mt) REVERT: E 227 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8243 (tt) REVERT: E 474 MET cc_start: 0.6431 (ppp) cc_final: 0.5943 (ppp) REVERT: E 562 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7726 (t0) REVERT: F 274 MET cc_start: 0.8679 (mmp) cc_final: 0.8446 (mmm) REVERT: F 349 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7705 (m110) REVERT: F 474 MET cc_start: 0.0738 (OUTLIER) cc_final: 0.0253 (mmm) outliers start: 102 outliers final: 71 residues processed: 249 average time/residue: 0.3552 time to fit residues: 138.1842 Evaluate side-chains 226 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 150 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 56 ASP Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 187 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 214 optimal weight: 30.0000 chunk 173 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 63 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: A 5 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 HIS F 349 ASN F 562 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22475 Z= 0.314 Angle : 0.598 13.921 30932 Z= 0.301 Chirality : 0.042 0.207 3604 Planarity : 0.004 0.063 3630 Dihedral : 14.695 175.430 4291 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 5.09 % Allowed : 19.09 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.31 (0.16), residues: 2541 helix: 0.15 (0.16), residues: 1037 sheet: -0.93 (0.29), residues: 322 loop : -1.77 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.006 0.001 HIS A 572 PHE 0.018 0.001 PHE A 652 TYR 0.015 0.001 TYR A 788 ARG 0.005 0.000 ARG F 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 160 time to evaluate : 2.415 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7760 (tpp80) cc_final: 0.7507 (ttm-80) REVERT: A 160 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7832 (ptmm) REVERT: A 450 ILE cc_start: 0.8736 (tp) cc_final: 0.8340 (tp) REVERT: A 822 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: B 62 MET cc_start: 0.8602 (tmm) cc_final: 0.8397 (tmm) REVERT: B 69 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8172 (tm-30) REVERT: B 70 MET cc_start: 0.7822 (ttm) cc_final: 0.7529 (mtt) REVERT: C 34 GLN cc_start: 0.8112 (tp40) cc_final: 0.7816 (tp40) REVERT: C 69 ASN cc_start: 0.7934 (t0) cc_final: 0.7692 (t0) REVERT: D 80 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7863 (mtm-85) REVERT: D 99 ASP cc_start: 0.8225 (t0) cc_final: 0.7982 (t0) REVERT: D 157 GLN cc_start: 0.8286 (mm110) cc_final: 0.8011 (mm110) REVERT: E 163 LEU cc_start: 0.9173 (mt) cc_final: 0.8775 (mt) REVERT: E 227 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8260 (tt) REVERT: E 262 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8523 (m-80) REVERT: E 474 MET cc_start: 0.6514 (ppp) cc_final: 0.5962 (ppp) REVERT: E 562 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7892 (t0) REVERT: F 274 MET cc_start: 0.8700 (mmp) cc_final: 0.8279 (mmp) REVERT: F 474 MET cc_start: 0.0661 (OUTLIER) cc_final: 0.0177 (mmm) REVERT: F 498 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.4732 (pt0) REVERT: F 506 TRP cc_start: 0.4149 (OUTLIER) cc_final: 0.3222 (p90) outliers start: 112 outliers final: 81 residues processed: 259 average time/residue: 0.3426 time to fit residues: 137.4884 Evaluate side-chains 238 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 149 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 253 TYR Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 448 ILE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 572 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 147 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 251 optimal weight: 20.0000 chunk 208 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 81 GLN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22475 Z= 0.179 Angle : 0.544 13.864 30932 Z= 0.271 Chirality : 0.039 0.204 3604 Planarity : 0.003 0.062 3630 Dihedral : 14.345 179.430 4283 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.73 % Allowed : 20.41 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.97 (0.17), residues: 2541 helix: 0.47 (0.17), residues: 1028 sheet: -0.76 (0.29), residues: 317 loop : -1.61 (0.17), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.003 0.001 HIS A 309 PHE 0.016 0.001 PHE A 652 TYR 0.020 0.001 TYR A 80 ARG 0.005 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 156 time to evaluate : 2.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7654 (tpp80) cc_final: 0.6826 (tpp80) REVERT: A 160 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7678 (ptmm) REVERT: A 450 ILE cc_start: 0.8594 (tp) cc_final: 0.8211 (tp) REVERT: A 463 MET cc_start: 0.7706 (ttt) cc_final: 0.7155 (ttt) REVERT: B 55 MET cc_start: 0.6533 (tpt) cc_final: 0.6140 (tpt) REVERT: B 69 GLN cc_start: 0.8712 (tm-30) cc_final: 0.8166 (tm-30) REVERT: B 70 MET cc_start: 0.7793 (ttm) cc_final: 0.7547 (mtt) REVERT: C 34 GLN cc_start: 0.8013 (tp40) cc_final: 0.7813 (tp40) REVERT: C 69 ASN cc_start: 0.7837 (t0) cc_final: 0.7608 (t0) REVERT: D 157 GLN cc_start: 0.8249 (mm110) cc_final: 0.7992 (mm110) REVERT: E 262 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8551 (m-80) REVERT: E 474 MET cc_start: 0.6294 (ppp) cc_final: 0.5709 (ppp) REVERT: E 562 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7621 (t0) REVERT: F 274 MET cc_start: 0.8626 (mmp) cc_final: 0.8343 (mmm) REVERT: F 351 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8337 (t) REVERT: F 474 MET cc_start: 0.1031 (mmt) cc_final: 0.0522 (mmm) REVERT: F 498 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.4762 (pt0) outliers start: 82 outliers final: 63 residues processed: 227 average time/residue: 0.3508 time to fit residues: 123.7467 Evaluate side-chains 217 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 149 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 426 CYS Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 211 optimal weight: 0.0060 chunk 140 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22475 Z= 0.303 Angle : 0.579 13.850 30932 Z= 0.291 Chirality : 0.041 0.204 3604 Planarity : 0.004 0.063 3630 Dihedral : 14.235 179.074 4272 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.27 % Allowed : 20.05 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.00 (0.17), residues: 2541 helix: 0.40 (0.17), residues: 1036 sheet: -0.69 (0.30), residues: 315 loop : -1.62 (0.17), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 916 HIS 0.006 0.001 HIS A 572 PHE 0.017 0.001 PHE A 652 TYR 0.015 0.001 TYR A 788 ARG 0.006 0.000 ARG A 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 151 time to evaluate : 2.515 Fit side-chains revert: symmetry clash REVERT: A 77 PHE cc_start: 0.7952 (t80) cc_final: 0.7657 (t80) REVERT: A 160 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7674 (ptmm) REVERT: A 450 ILE cc_start: 0.8748 (tp) cc_final: 0.8306 (tp) REVERT: A 822 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: B 55 MET cc_start: 0.6547 (tpt) cc_final: 0.6159 (tpt) REVERT: B 69 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8192 (tm-30) REVERT: B 70 MET cc_start: 0.7832 (ttm) cc_final: 0.7583 (mtt) REVERT: C 69 ASN cc_start: 0.7897 (t0) cc_final: 0.7654 (t0) REVERT: E 262 PHE cc_start: 0.8956 (OUTLIER) cc_final: 0.8514 (m-80) REVERT: E 404 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.6911 (mm110) REVERT: E 474 MET cc_start: 0.6355 (ppp) cc_final: 0.5737 (ppp) REVERT: E 562 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7812 (t0) REVERT: F 95 ASN cc_start: 0.8176 (OUTLIER) cc_final: 0.7873 (p0) REVERT: F 351 THR cc_start: 0.8766 (p) cc_final: 0.8383 (t) REVERT: F 474 MET cc_start: 0.0613 (OUTLIER) cc_final: 0.0046 (mmm) REVERT: F 498 GLU cc_start: 0.5674 (OUTLIER) cc_final: 0.4763 (pt0) outliers start: 94 outliers final: 70 residues processed: 234 average time/residue: 0.3506 time to fit residues: 128.5843 Evaluate side-chains 227 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 149 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 262 PHE Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 95 ASN Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 426 CYS Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 22475 Z= 0.190 Angle : 0.535 13.809 30932 Z= 0.269 Chirality : 0.039 0.201 3604 Planarity : 0.003 0.062 3630 Dihedral : 14.073 179.578 4272 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.82 % Allowed : 20.50 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.79 (0.17), residues: 2541 helix: 0.57 (0.17), residues: 1035 sheet: -0.60 (0.30), residues: 315 loop : -1.49 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.017 0.001 PHE A 77 TYR 0.013 0.001 TYR A 80 ARG 0.004 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 156 time to evaluate : 2.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7668 (ptmm) REVERT: A 450 ILE cc_start: 0.8661 (tp) cc_final: 0.8242 (tp) REVERT: A 463 MET cc_start: 0.7755 (ttt) cc_final: 0.7195 (ttt) REVERT: A 815 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: B 55 MET cc_start: 0.6497 (tpt) cc_final: 0.6079 (tpt) REVERT: B 62 MET cc_start: 0.8396 (tmm) cc_final: 0.7977 (tmm) REVERT: B 69 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8148 (tm-30) REVERT: B 70 MET cc_start: 0.7829 (ttm) cc_final: 0.7571 (mtt) REVERT: C 34 GLN cc_start: 0.7909 (tp40) cc_final: 0.7577 (tp40) REVERT: C 38 ASP cc_start: 0.7169 (m-30) cc_final: 0.6949 (m-30) REVERT: C 69 ASN cc_start: 0.7853 (t0) cc_final: 0.7630 (t0) REVERT: E 474 MET cc_start: 0.6350 (ppp) cc_final: 0.5815 (ppp) REVERT: E 562 ASN cc_start: 0.8009 (OUTLIER) cc_final: 0.7617 (t0) REVERT: F 349 ASN cc_start: 0.7947 (OUTLIER) cc_final: 0.7640 (m110) REVERT: F 351 THR cc_start: 0.8762 (p) cc_final: 0.8321 (t) REVERT: F 474 MET cc_start: 0.0875 (mmt) cc_final: 0.0301 (mmm) REVERT: F 498 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.4842 (pt0) REVERT: F 576 MET cc_start: 0.2488 (mmp) cc_final: 0.2128 (tpp) outliers start: 84 outliers final: 66 residues processed: 229 average time/residue: 0.3666 time to fit residues: 130.9015 Evaluate side-chains 223 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 152 time to evaluate : 2.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 385 SER Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 559 ASN Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 349 ASN Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 426 CYS Chi-restraints excluded: chain F residue 484 VAL Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.4980 chunk 240 optimal weight: 8.9990 chunk 219 optimal weight: 0.3980 chunk 233 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 71 optimal weight: 0.0980 chunk 211 optimal weight: 9.9990 chunk 220 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 349 ASN ** F 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 22475 Z= 0.149 Angle : 0.533 13.755 30932 Z= 0.264 Chirality : 0.039 0.199 3604 Planarity : 0.003 0.062 3630 Dihedral : 13.855 179.145 4266 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.05 % Allowed : 21.36 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.59 (0.17), residues: 2541 helix: 0.74 (0.17), residues: 1039 sheet: -0.47 (0.30), residues: 309 loop : -1.38 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 617 HIS 0.003 0.000 HIS A 309 PHE 0.014 0.001 PHE A 652 TYR 0.009 0.001 TYR F 217 ARG 0.004 0.000 ARG D 75 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 159 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7647 (ptmm) REVERT: A 450 ILE cc_start: 0.8594 (tp) cc_final: 0.8211 (tp) REVERT: A 463 MET cc_start: 0.7567 (ttt) cc_final: 0.6987 (ttt) REVERT: A 815 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: A 822 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: B 55 MET cc_start: 0.6477 (tpt) cc_final: 0.6066 (tpt) REVERT: B 62 MET cc_start: 0.8389 (tmm) cc_final: 0.7949 (tmm) REVERT: B 69 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8169 (tm-30) REVERT: B 70 MET cc_start: 0.7808 (ttm) cc_final: 0.7575 (mtt) REVERT: C 34 GLN cc_start: 0.7833 (tp40) cc_final: 0.7500 (tp40) REVERT: E 474 MET cc_start: 0.6281 (ppp) cc_final: 0.5728 (ppp) REVERT: E 562 ASN cc_start: 0.7991 (OUTLIER) cc_final: 0.7611 (t0) REVERT: F 351 THR cc_start: 0.8622 (p) cc_final: 0.8266 (t) REVERT: F 474 MET cc_start: 0.0859 (mmt) cc_final: 0.0310 (mmm) REVERT: F 498 GLU cc_start: 0.5746 (OUTLIER) cc_final: 0.4826 (pt0) outliers start: 67 outliers final: 55 residues processed: 213 average time/residue: 0.3594 time to fit residues: 118.3686 Evaluate side-chains 209 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 149 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 259 optimal weight: 20.0000 chunk 238 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 GLN ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22475 Z= 0.274 Angle : 0.567 13.738 30932 Z= 0.283 Chirality : 0.040 0.199 3604 Planarity : 0.004 0.062 3630 Dihedral : 13.872 178.261 4261 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.05 % Allowed : 21.41 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.17), residues: 2541 helix: 0.67 (0.17), residues: 1036 sheet: -0.44 (0.30), residues: 309 loop : -1.40 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.016 0.001 PHE A 652 TYR 0.015 0.001 TYR B 71 ARG 0.005 0.000 ARG B 75 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 149 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7645 (ptmm) REVERT: A 450 ILE cc_start: 0.8705 (tp) cc_final: 0.8238 (tp) REVERT: A 815 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7547 (mm-40) REVERT: A 822 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: B 55 MET cc_start: 0.6541 (tpt) cc_final: 0.6120 (tpt) REVERT: B 69 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 70 MET cc_start: 0.7836 (ttm) cc_final: 0.7583 (mtt) REVERT: C 34 GLN cc_start: 0.7802 (tp40) cc_final: 0.7507 (tp40) REVERT: E 474 MET cc_start: 0.6316 (ppp) cc_final: 0.5790 (ppp) REVERT: E 549 THR cc_start: 0.8729 (m) cc_final: 0.8522 (m) REVERT: E 562 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7855 (t0) REVERT: F 351 THR cc_start: 0.8771 (p) cc_final: 0.8371 (t) REVERT: F 474 MET cc_start: 0.0907 (mmt) cc_final: 0.0363 (mmm) REVERT: F 498 GLU cc_start: 0.5833 (OUTLIER) cc_final: 0.4884 (pt0) REVERT: F 506 TRP cc_start: 0.3276 (OUTLIER) cc_final: 0.2207 (p90) REVERT: F 576 MET cc_start: 0.2311 (mmp) cc_final: 0.2091 (tpp) outliers start: 67 outliers final: 58 residues processed: 206 average time/residue: 0.3542 time to fit residues: 113.0129 Evaluate side-chains 213 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 149 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 815 GLN Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 822 GLN Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 178 ARG Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 320 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 423 ASN Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 451 THR Chi-restraints excluded: chain E residue 458 ASP Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 521 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 97 CYS Chi-restraints excluded: chain F residue 116 ASN Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 356 VAL Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 426 CYS Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 498 GLU Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 526 LEU Chi-restraints excluded: chain F residue 562 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.4980 chunk 219 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 206 optimal weight: 0.0470 chunk 86 optimal weight: 0.6980 chunk 212 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 243 GLN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 516 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 = 0.3980 r_free = 0.3980 target = 0.134290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092847 restraints weight = 35657.257| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.47 r_work: 0.3229 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22475 Z= 0.199 Angle : 0.538 13.721 30932 Z= 0.268 Chirality : 0.039 0.197 3604 Planarity : 0.003 0.062 3630 Dihedral : 13.781 175.643 4261 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.05 % Allowed : 21.36 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.56 (0.17), residues: 2541 helix: 0.74 (0.17), residues: 1038 sheet: -0.41 (0.30), residues: 309 loop : -1.36 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 617 HIS 0.004 0.001 HIS A 309 PHE 0.015 0.001 PHE A 652 TYR 0.016 0.001 TYR B 71 ARG 0.004 0.000 ARG B 75 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5028.56 seconds wall clock time: 91 minutes 19.56 seconds (5479.56 seconds total)