Starting phenix.real_space_refine on Sun Mar 17 08:11:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re2_24431/03_2024/7re2_24431_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re2_24431/03_2024/7re2_24431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re2_24431/03_2024/7re2_24431.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re2_24431/03_2024/7re2_24431.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re2_24431/03_2024/7re2_24431_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re2_24431/03_2024/7re2_24431_updated.pdb" } resolution = 3.17 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= 0.002 sd= 0.099 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 5 6.06 5 Al 1 5.89 5 P 75 5.49 5 Mg 2 5.21 5 S 117 5.16 5 C 10578 2.51 5 N 2881 2.21 5 O 3434 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 60": "OD1" <-> "OD2" Residue "A PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 917": "OE1" <-> "OE2" Residue "A TYR 921": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B ASP 101": "OD1" <-> "OD2" Residue "B TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 5": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 369": "OD1" <-> "OD2" Residue "E PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17096 Number of models: 1 Model: "" Number of chains: 9 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: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 177} 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: 4557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4557 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} 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: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 789 Classifications: {'RNA': 37} Modifications used: {'rna3p_pur': 20, 'rna3p_pyr': 17} Link IDs: {'rna3p': 36} Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 91 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 2, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 71 Unusual residues: {' MG': 1, ' ZN': 3, '1N7': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 85.918 102.516 109.737 1.00 38.59 S ATOM 2495 SG CYS A 306 86.531 101.117 113.281 1.00 34.60 S ATOM 2527 SG CYS A 310 84.787 104.460 112.792 1.00 36.67 S ATOM 3935 SG CYS A 487 84.393 87.754 95.382 1.00 37.43 S ATOM 5188 SG CYS A 645 85.593 86.047 98.607 1.00 43.02 S ATOM 5194 SG CYS A 646 86.107 89.800 98.006 1.00 40.03 S ATOM 10896 SG CYS E 5 37.457 84.570 46.824 1.00 79.46 S ATOM 10917 SG CYS E 8 35.387 83.599 48.135 1.00 83.51 S ATOM 11055 SG CYS E 26 36.939 80.207 47.399 1.00 82.68 S ATOM 11076 SG CYS E 29 35.959 82.112 44.541 1.00 87.27 S ATOM 11241 SG CYS E 50 59.124 68.782 43.616 1.00116.45 S ATOM 11271 SG CYS E 55 60.774 69.332 40.436 1.00119.99 S ATOM 11404 SG CYS E 72 58.262 66.287 40.676 1.00122.40 S ATOM 10978 SG CYS E 16 47.202 83.633 40.362 1.00 93.01 S ATOM 10993 SG CYS E 19 46.267 87.298 39.423 1.00100.24 S Time building chain proxies: 9.28, per 1000 atoms: 0.54 Number of scatterers: 17096 At special positions: 0 Unit cell: (104.86, 154.08, 174.41, 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 5 29.99 S 117 16.00 P 75 15.00 Al 1 13.00 Mg 2 11.99 F 3 9.00 O 3434 8.00 N 2881 7.00 C 10578 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.83 Conformation dependent library (CDL) restraints added in 3.1 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 E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " Number of angles added : 16 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 79 helices and 16 sheets defined 42.7% alpha, 8.9% beta 34 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 7.80 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.519A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 141 through 148 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 199 removed outlier: 4.714A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (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 247 removed outlier: 3.741A pdb=" N LEU A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.021A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' 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 286 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 304 through 319 removed outlier: 3.931A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 379 through 383 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 448 through 458 removed outlier: 4.146A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.768A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' 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 removed outlier: 3.536A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 579 removed outlier: 4.044A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.806A 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 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 648 through 662 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 789 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 871 Proline residue: A 868 - end of helix removed outlier: 4.479A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 4.246A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.878A 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 925 removed outlier: 4.168A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 32 through 96 removed outlier: 3.948A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix removed outlier: 3.603A pdb=" N THR B 124 " --> pdb=" O PRO B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'C' and resid 3 through 19 removed outlier: 3.541A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.632A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.593A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 72 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 101 through 112 Processing helix chain 'D' and resid 135 through 141 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' 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 34 Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 94 through 96 No H-bonds generated for 'chain 'E' and resid 94 through 96' Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.667A pdb=" N ASN E 107 " --> pdb=" O VAL E 103 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 108 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 123 Processing helix chain 'E' and resid 128 through 148 removed outlier: 3.941A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 274 removed outlier: 3.829A pdb=" N VAL E 266 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA E 267 " --> pdb=" O SER E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 298 removed outlier: 4.013A 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 376 through 378 No H-bonds generated for 'chain 'E' and resid 376 through 378' 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 454 removed outlier: 4.673A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 498 Processing helix chain 'E' and resid 504 through 506 No H-bonds generated for 'chain 'E' and resid 504 through 506' Processing helix chain 'E' and resid 516 through 526 removed outlier: 4.232A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 536 No H-bonds generated for 'chain 'E' and resid 533 through 536' Processing helix chain 'E' and resid 558 through 567 removed outlier: 4.200A pdb=" N ARG E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 584 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 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 99 through 105 removed outlier: 3.579A pdb=" N PHE A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) 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 540 through 544 Processing sheet with id= F, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= G, first strand: chain 'A' and resid 666 through 668 removed outlier: 3.501A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= I, first strand: chain 'B' and resid 127 through 132 removed outlier: 5.921A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.501A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= L, first strand: chain 'E' and resid 162 through 164 Processing sheet with id= M, first strand: chain 'E' and resid 197 through 199 Processing sheet with id= N, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.735A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 366 through 368 Processing sheet with id= P, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.293A pdb=" N ILE E 572 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N MET E 474 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS E 574 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL E 544 " --> pdb=" O GLY E 571 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER E 513 " --> pdb=" O GLN E 531 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 168 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 6.73 Time building geometry restraints manager: 8.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4780 1.33 - 1.45: 3334 1.45 - 1.57: 9123 1.57 - 1.69: 197 1.69 - 1.81: 175 Bond restraints: 17609 Sorted by residual: bond pdb=" F2 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.66e+01 bond pdb=" F1 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" F3 AF3 E 706 " pdb="AL AF3 E 706 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" C17 1N7 A1005 " pdb=" C18 1N7 A1005 " ideal model delta sigma weight residual 1.528 1.636 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C17 1N7 A1006 " pdb=" C18 1N7 A1006 " ideal model delta sigma weight residual 1.528 1.631 -0.103 2.00e-02 2.50e+03 2.65e+01 ... (remaining 17604 not shown) Histogram of bond angle deviations from ideal: 97.74 - 105.45: 631 105.45 - 113.17: 9872 113.17 - 120.88: 8563 120.88 - 128.59: 5040 128.59 - 136.31: 168 Bond angle restraints: 24274 Sorted by residual: angle pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta sigma weight residual 121.70 134.30 -12.60 1.80e+00 3.09e-01 4.90e+01 angle pdb=" N ILE E 432 " pdb=" CA ILE E 432 " pdb=" C ILE E 432 " ideal model delta sigma weight residual 113.47 109.50 3.97 1.01e+00 9.80e-01 1.54e+01 angle pdb=" C4 1N7 A1005 " pdb=" C5 1N7 A1005 " pdb=" C9 1N7 A1005 " ideal model delta sigma weight residual 117.60 105.93 11.67 3.00e+00 1.11e-01 1.51e+01 angle pdb=" C LEU A 758 " pdb=" N SER A 759 " pdb=" CA SER A 759 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" N LYS E 189 " pdb=" CA LYS E 189 " pdb=" C LYS E 189 " ideal model delta sigma weight residual 110.80 118.73 -7.93 2.13e+00 2.20e-01 1.39e+01 ... (remaining 24269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 10437 35.83 - 71.65: 291 71.65 - 107.48: 50 107.48 - 143.30: 9 143.30 - 179.13: 4 Dihedral angle restraints: 10791 sinusoidal: 4972 harmonic: 5819 Sorted by residual: dihedral pdb=" CA LYS E 189 " pdb=" C LYS E 189 " pdb=" N ASN E 190 " pdb=" CA ASN E 190 " ideal model delta harmonic sigma weight residual 0.00 39.02 -39.02 0 5.00e+00 4.00e-02 6.09e+01 dihedral pdb=" O2A ADP A1004 " pdb=" O3A ADP A1004 " pdb=" PA ADP A1004 " pdb=" PB ADP A1004 " ideal model delta sinusoidal sigma weight residual -60.00 119.13 -179.13 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP A1004 " pdb=" O5' ADP A1004 " pdb=" PA ADP A1004 " pdb=" O2A ADP A1004 " ideal model delta sinusoidal sigma weight residual 300.00 125.31 174.69 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 10788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.028: 2828 1.028 - 2.055: 0 2.055 - 3.083: 0 3.083 - 4.110: 0 4.110 - 5.138: 2 Chirality restraints: 2830 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 2.71 -5.14 2.00e-01 2.50e+01 6.60e+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 -2.59 5.12 2.00e-01 2.50e+01 6.56e+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 2.81 -0.41 2.00e-01 2.50e+01 4.23e+00 ... (remaining 2827 not shown) Planarity restraints: 2811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE D 132 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO D 133 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 231 " 0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO A 232 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 926 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 927 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 927 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 927 " 0.017 5.00e-02 4.00e+02 ... (remaining 2808 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 123 2.53 - 3.12: 13025 3.12 - 3.71: 27590 3.71 - 4.31: 38713 4.31 - 4.90: 63344 Nonbonded interactions: 142795 Sorted by model distance: nonbonded pdb="MG MG A1003 " pdb=" O1A ADP A1004 " model vdw 1.932 2.170 nonbonded pdb=" O3B ADP E 704 " pdb="MG MG E 705 " model vdw 1.994 2.170 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1003 " model vdw 2.003 2.170 nonbonded pdb=" OG SER E 289 " pdb="MG MG E 705 " model vdw 2.039 2.170 nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1003 " model vdw 2.048 2.170 ... (remaining 142790 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)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.020 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 55.980 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.007 0.163 17609 Z= 0.403 Angle : 0.650 12.600 24274 Z= 0.334 Chirality : 0.145 5.138 2830 Planarity : 0.003 0.038 2811 Dihedral : 16.681 179.128 7033 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.42 % Allowed : 7.62 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1953 helix: 0.72 (0.18), residues: 848 sheet: -0.99 (0.34), residues: 223 loop : -1.26 (0.20), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 916 HIS 0.008 0.001 HIS A 309 PHE 0.016 0.002 PHE A 741 TYR 0.016 0.001 TYR A 788 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 177 time to evaluate : 1.957 Fit side-chains revert: symmetry clash REVERT: A 221 ASP cc_start: 0.7776 (p0) cc_final: 0.7570 (p0) REVERT: A 258 ASP cc_start: 0.7065 (t0) cc_final: 0.6801 (t0) REVERT: D 70 MET cc_start: 0.7958 (tpt) cc_final: 0.7752 (tpt) outliers start: 41 outliers final: 25 residues processed: 217 average time/residue: 0.3124 time to fit residues: 100.7469 Evaluate side-chains 180 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 161 ASP Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 562 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 80 optimal weight: 0.2980 chunk 156 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17609 Z= 0.394 Angle : 0.595 12.686 24274 Z= 0.302 Chirality : 0.042 0.207 2830 Planarity : 0.004 0.040 2811 Dihedral : 15.289 178.318 3511 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.36 % Allowed : 10.92 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.19), residues: 1953 helix: 0.57 (0.18), residues: 863 sheet: -0.88 (0.35), residues: 213 loop : -1.24 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.009 0.001 HIS C 36 PHE 0.018 0.002 PHE A 741 TYR 0.017 0.002 TYR A 788 ARG 0.004 0.000 ARG A 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 162 time to evaluate : 1.661 Fit side-chains revert: symmetry clash REVERT: A 258 ASP cc_start: 0.7148 (t0) cc_final: 0.6879 (t0) REVERT: B 43 ASN cc_start: 0.7284 (t0) cc_final: 0.7023 (t0) REVERT: B 104 ASN cc_start: 0.8100 (m-40) cc_final: 0.7648 (m110) outliers start: 57 outliers final: 37 residues processed: 208 average time/residue: 0.2979 time to fit residues: 93.0325 Evaluate side-chains 190 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 153 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 608 ASP Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 426 CYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 151 optimal weight: 40.0000 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 181 optimal weight: 4.9990 chunk 196 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17609 Z= 0.253 Angle : 0.528 12.662 24274 Z= 0.266 Chirality : 0.039 0.205 2830 Planarity : 0.003 0.035 2811 Dihedral : 14.788 174.514 3506 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.48 % Allowed : 11.81 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 1953 helix: 0.67 (0.18), residues: 857 sheet: -0.80 (0.34), residues: 219 loop : -1.14 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.016 0.001 PHE A 652 TYR 0.014 0.001 TYR A 788 ARG 0.004 0.000 ARG D 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 161 time to evaluate : 1.939 Fit side-chains revert: symmetry clash REVERT: B 104 ASN cc_start: 0.8065 (m-40) cc_final: 0.7679 (m110) REVERT: D 38 LEU cc_start: 0.7105 (mt) cc_final: 0.6902 (tp) outliers start: 59 outliers final: 37 residues processed: 209 average time/residue: 0.2895 time to fit residues: 91.3648 Evaluate side-chains 192 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 30.0000 chunk 136 optimal weight: 5.9990 chunk 94 optimal weight: 50.0000 chunk 20 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 182 optimal weight: 20.0000 chunk 193 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN E 464 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17609 Z= 0.365 Angle : 0.564 12.743 24274 Z= 0.287 Chirality : 0.041 0.207 2830 Planarity : 0.004 0.042 2811 Dihedral : 14.546 174.778 3505 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.60 % Allowed : 13.40 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.52 (0.19), residues: 1953 helix: 0.57 (0.18), residues: 857 sheet: -0.67 (0.35), residues: 207 loop : -1.14 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 916 HIS 0.009 0.001 HIS C 36 PHE 0.018 0.002 PHE A 741 TYR 0.017 0.001 TYR A 788 ARG 0.006 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 159 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 CYS cc_start: 0.8257 (p) cc_final: 0.8007 (p) REVERT: A 110 MET cc_start: 0.8131 (mmm) cc_final: 0.7613 (mmm) REVERT: A 445 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8381 (p0) REVERT: B 104 ASN cc_start: 0.8073 (m-40) cc_final: 0.7741 (m110) REVERT: E 376 ILE cc_start: 0.6200 (OUTLIER) cc_final: 0.5914 (pp) outliers start: 61 outliers final: 48 residues processed: 205 average time/residue: 0.3002 time to fit residues: 92.1329 Evaluate side-chains 205 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 155 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 309 CYS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 143 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 133 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17609 Z= 0.234 Angle : 0.515 12.699 24274 Z= 0.261 Chirality : 0.039 0.205 2830 Planarity : 0.003 0.040 2811 Dihedral : 14.356 173.293 3505 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.25 % Allowed : 14.23 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.39 (0.19), residues: 1953 helix: 0.70 (0.18), residues: 858 sheet: -0.64 (0.34), residues: 219 loop : -1.09 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.010 0.001 HIS E 464 PHE 0.015 0.001 PHE A 652 TYR 0.013 0.001 TYR A 788 ARG 0.005 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 165 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 CYS cc_start: 0.8210 (p) cc_final: 0.7884 (p) REVERT: A 110 MET cc_start: 0.8095 (mmm) cc_final: 0.7856 (mmm) REVERT: A 445 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8361 (p0) REVERT: B 43 ASN cc_start: 0.7442 (m-40) cc_final: 0.7175 (t0) REVERT: B 104 ASN cc_start: 0.8035 (m-40) cc_final: 0.7719 (m110) REVERT: E 376 ILE cc_start: 0.6121 (OUTLIER) cc_final: 0.5838 (pp) outliers start: 55 outliers final: 43 residues processed: 205 average time/residue: 0.2864 time to fit residues: 88.6547 Evaluate side-chains 204 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17609 Z= 0.200 Angle : 0.502 12.709 24274 Z= 0.253 Chirality : 0.038 0.204 2830 Planarity : 0.003 0.040 2811 Dihedral : 14.177 173.222 3498 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.25 % Allowed : 15.41 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.26 (0.19), residues: 1953 helix: 0.80 (0.18), residues: 857 sheet: -0.44 (0.35), residues: 207 loop : -1.03 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.015 0.001 PHE A 741 TYR 0.014 0.001 TYR E 31 ARG 0.006 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 168 time to evaluate : 1.829 Fit side-chains revert: symmetry clash REVERT: A 12 CYS cc_start: 0.8186 (p) cc_final: 0.7844 (p) REVERT: A 110 MET cc_start: 0.8086 (mmm) cc_final: 0.7865 (mmm) REVERT: A 445 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.8338 (p0) REVERT: A 658 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: A 902 MET cc_start: 0.8586 (ttm) cc_final: 0.8377 (ttm) REVERT: B 43 ASN cc_start: 0.7498 (m-40) cc_final: 0.7196 (t0) REVERT: B 104 ASN cc_start: 0.8039 (m-40) cc_final: 0.7717 (m110) REVERT: D 38 LEU cc_start: 0.7100 (mt) cc_final: 0.6887 (tp) REVERT: D 155 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7127 (mm-30) REVERT: E 307 THR cc_start: 0.8194 (t) cc_final: 0.7912 (p) outliers start: 55 outliers final: 45 residues processed: 208 average time/residue: 0.2856 time to fit residues: 90.7980 Evaluate side-chains 207 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 160 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 309 CYS Chi-restraints excluded: chain E residue 365 GLU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 570 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 162 optimal weight: 8.9990 chunk 108 optimal weight: 3.9990 chunk 192 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17609 Z= 0.413 Angle : 0.584 12.768 24274 Z= 0.295 Chirality : 0.042 0.209 2830 Planarity : 0.004 0.041 2811 Dihedral : 14.183 178.060 3498 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.90 % Allowed : 15.35 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 1953 helix: 0.58 (0.18), residues: 858 sheet: -0.43 (0.36), residues: 195 loop : -1.12 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.010 0.001 HIS A 309 PHE 0.018 0.002 PHE A 741 TYR 0.019 0.002 TYR A 788 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 161 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 CYS cc_start: 0.8280 (p) cc_final: 0.7936 (p) REVERT: A 445 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8377 (p0) REVERT: B 43 ASN cc_start: 0.7523 (m-40) cc_final: 0.7123 (t0) REVERT: B 104 ASN cc_start: 0.8077 (m-40) cc_final: 0.7792 (m110) REVERT: E 257 ASN cc_start: 0.6729 (t0) cc_final: 0.6498 (p0) outliers start: 66 outliers final: 57 residues processed: 210 average time/residue: 0.2898 time to fit residues: 92.3046 Evaluate side-chains 216 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 158 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 682 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 871 LYS Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 309 CYS Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 365 GLU Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 570 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.0270 chunk 76 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17609 Z= 0.139 Angle : 0.492 12.681 24274 Z= 0.248 Chirality : 0.038 0.204 2830 Planarity : 0.003 0.040 2811 Dihedral : 14.107 178.301 3498 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.54 % Allowed : 16.77 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.13 (0.19), residues: 1953 helix: 0.89 (0.18), residues: 851 sheet: -0.20 (0.36), residues: 183 loop : -0.96 (0.20), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.004 0.001 HIS A 309 PHE 0.014 0.001 PHE E 373 TYR 0.010 0.001 TYR A 884 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 166 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 CYS cc_start: 0.8154 (p) cc_final: 0.7800 (p) REVERT: B 104 ASN cc_start: 0.7987 (m-40) cc_final: 0.7693 (m110) REVERT: C 21 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7508 (mtm110) REVERT: D 38 LEU cc_start: 0.7091 (mt) cc_final: 0.6877 (tp) REVERT: D 155 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7188 (mm-30) REVERT: E 307 THR cc_start: 0.8148 (t) cc_final: 0.7860 (p) outliers start: 43 outliers final: 39 residues processed: 201 average time/residue: 0.2957 time to fit residues: 91.5284 Evaluate side-chains 202 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 163 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 309 CYS Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 179 optimal weight: 40.0000 chunk 108 optimal weight: 0.0270 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 162 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 189 optimal weight: 20.0000 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 17609 Z= 0.450 Angle : 0.602 12.800 24274 Z= 0.305 Chirality : 0.043 0.210 2830 Planarity : 0.004 0.046 2811 Dihedral : 14.080 179.270 3493 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.31 % Allowed : 16.77 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.40 (0.19), residues: 1953 helix: 0.63 (0.18), residues: 857 sheet: -0.44 (0.35), residues: 203 loop : -1.06 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 916 HIS 0.011 0.001 HIS A 309 PHE 0.019 0.002 PHE A 741 TYR 0.020 0.002 TYR A 788 ARG 0.008 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 160 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 CYS cc_start: 0.8272 (p) cc_final: 0.7931 (p) REVERT: A 445 ASP cc_start: 0.8666 (OUTLIER) cc_final: 0.8365 (p0) REVERT: A 626 MET cc_start: 0.8477 (ttm) cc_final: 0.8224 (ttp) REVERT: A 883 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8596 (tp) REVERT: B 43 ASN cc_start: 0.7524 (m-40) cc_final: 0.7092 (t0) REVERT: B 104 ASN cc_start: 0.8038 (m-40) cc_final: 0.7740 (m110) REVERT: C 21 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7531 (mtm110) REVERT: E 257 ASN cc_start: 0.6697 (t0) cc_final: 0.6482 (p0) outliers start: 56 outliers final: 45 residues processed: 207 average time/residue: 0.2836 time to fit residues: 89.0421 Evaluate side-chains 205 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 158 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 481 ASP Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 848 VAL Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 309 CYS Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 199 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 158 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17609 Z= 0.208 Angle : 0.519 12.694 24274 Z= 0.261 Chirality : 0.039 0.205 2830 Planarity : 0.003 0.040 2811 Dihedral : 14.011 175.782 3492 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.60 % Allowed : 17.71 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.26 (0.19), residues: 1953 helix: 0.79 (0.18), residues: 857 sheet: -0.51 (0.34), residues: 215 loop : -1.01 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.015 0.001 PHE A 652 TYR 0.011 0.001 TYR A 788 ARG 0.010 0.000 ARG D 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3906 Ramachandran restraints generated. 1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 162 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 CYS cc_start: 0.8212 (p) cc_final: 0.7868 (p) REVERT: A 626 MET cc_start: 0.8438 (ttm) cc_final: 0.8189 (ttp) REVERT: A 883 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8458 (tp) REVERT: B 90 MET cc_start: 0.8770 (ttp) cc_final: 0.8401 (ttp) REVERT: B 104 ASN cc_start: 0.8027 (m-40) cc_final: 0.7707 (m110) REVERT: C 21 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7535 (mtm110) REVERT: D 155 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7130 (mm-30) REVERT: E 307 THR cc_start: 0.8207 (t) cc_final: 0.7905 (p) outliers start: 44 outliers final: 41 residues processed: 201 average time/residue: 0.2968 time to fit residues: 90.3724 Evaluate side-chains 201 residues out of total 1717 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 2.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 258 ILE Chi-restraints excluded: chain E residue 309 CYS Chi-restraints excluded: chain E residue 342 CYS Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 404 GLN Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 526 LEU Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain E residue 572 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 158 optimal weight: 0.0270 chunk 66 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 139 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 403 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.157772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.104956 restraints weight = 25522.342| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.37 r_work: 0.3187 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17609 Z= 0.145 Angle : 0.490 12.711 24274 Z= 0.244 Chirality : 0.037 0.204 2830 Planarity : 0.003 0.040 2811 Dihedral : 13.833 172.312 3492 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.54 % Allowed : 18.00 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.03 (0.19), residues: 1953 helix: 1.04 (0.18), residues: 852 sheet: -0.13 (0.37), residues: 183 loop : -0.90 (0.20), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS A 309 PHE 0.013 0.001 PHE E 373 TYR 0.009 0.001 TYR E 31 ARG 0.004 0.000 ARG B 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3708.28 seconds wall clock time: 67 minutes 41.57 seconds (4061.57 seconds total)