Starting phenix.real_space_refine on Mon Mar 18 17:02:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/03_2024/7re0_24429_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/03_2024/7re0_24429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/03_2024/7re0_24429.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/03_2024/7re0_24429.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/03_2024/7re0_24429_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7re0_24429/03_2024/7re0_24429_updated.pdb" } resolution = 3.5 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= 0.011 sd= 1.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 Al 2 5.89 5 P 77 5.49 5 Mg 3 5.21 5 S 151 5.16 5 C 13390 2.51 5 N 3653 2.21 5 O 4287 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 10": "NH1" <-> "NH2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A ARG 249": "NH1" <-> "NH2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 665": "OE1" <-> "OE2" Residue "A TYR 728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 796": "OE1" <-> "OE2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A GLU 857": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 111": "NH1" <-> "NH2" Residue "C GLU 23": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "E PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 582": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "F PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21577 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 927, 7470 Classifications: {'peptide': 927} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 896} Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 576 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain: "D" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1415 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'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: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4550 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 559} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4550 Classifications: {'peptide': 590} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 558} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "F" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 35 Unusual residues: {' MG': 1, ' ZN': 3, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2454 SG CYS A 301 67.264 45.450 119.235 1.00 66.41 S ATOM 2495 SG CYS A 306 66.670 46.803 122.763 1.00 65.72 S ATOM 2527 SG CYS A 310 68.298 43.392 122.281 1.00 59.62 S ATOM 3935 SG CYS A 487 69.093 60.435 105.395 1.00 66.69 S ATOM 5188 SG CYS A 645 67.891 62.289 108.535 1.00 71.92 S ATOM 5194 SG CYS A 646 67.250 58.546 108.018 1.00 69.89 S ATOM 10896 SG CYS E 5 110.546 65.599 55.107 1.00 81.99 S ATOM 10917 SG CYS E 8 113.550 67.537 55.418 1.00 83.81 S ATOM 11055 SG CYS E 26 110.403 69.419 56.178 1.00 81.91 S ATOM 11076 SG CYS E 29 110.790 68.661 52.763 1.00 82.02 S ATOM 11241 SG CYS E 50 85.966 71.045 62.688 1.00 85.94 S ATOM 11271 SG CYS E 55 83.332 69.827 60.118 1.00 89.95 S ATOM 11404 SG CYS E 72 84.595 73.574 60.136 1.00 82.73 S ATOM 10978 SG CYS E 16 100.009 63.068 52.210 1.00 81.29 S ATOM 10993 SG CYS E 19 101.569 60.239 50.186 1.00 83.44 S ATOM 15446 SG CYS F 5 65.161 64.889 58.228 1.00 74.00 S ATOM 15467 SG CYS F 8 67.970 65.171 55.838 1.00 77.58 S ATOM 15605 SG CYS F 26 67.431 68.139 57.916 1.00 77.71 S ATOM 15626 SG CYS F 29 64.838 67.636 55.596 1.00 79.20 S ATOM 15791 SG CYS F 50 57.936 79.431 79.759 1.00 81.53 S ATOM 15821 SG CYS F 55 54.398 80.847 79.865 1.00 87.91 S ATOM 15954 SG CYS F 72 56.807 82.410 77.540 1.00 77.99 S ATOM 15528 SG CYS F 16 56.279 67.501 63.967 1.00 72.40 S ATOM 15543 SG CYS F 19 54.232 64.466 62.732 1.00 75.25 S Time building chain proxies: 11.15, per 1000 atoms: 0.52 Number of scatterers: 21577 At special positions: 0 Unit cell: (156.22, 150.87, 182.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 151 16.00 P 77 15.00 Al 2 13.00 Mg 3 11.99 F 6 9.00 O 4287 8.00 N 3653 7.00 C 13390 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: 9.69 Conformation dependent library (CDL) restraints added in 3.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 310 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 306 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 301 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 487 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 646 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 645 " pdb=" ZN E1000 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 8 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 26 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 5 " pdb="ZN ZN E1000 " - pdb=" SG CYS E 29 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 50 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 72 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 55 " pdb=" ZN E1002 " pdb="ZN ZN E1002 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E1002 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 19 " pdb="ZN ZN E1002 " - pdb=" SG CYS E 16 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " Number of angles added : 27 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4874 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 21 sheets defined 38.3% alpha, 8.9% beta 34 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 9.67 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.597A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 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: 3.676A pdb=" N ALA A 176 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG A 183 " --> pdb=" O GLU A 180 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN A 184 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N CYS A 193 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN A 198 " --> pdb=" O ALA A 195 " (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 Proline residue: A 243 - end of helix removed outlier: 4.022A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 removed outlier: 4.421A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 276 through 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 320 removed outlier: 3.804A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 378 through 384 Processing helix chain 'A' and resid 417 through 426 Processing helix chain 'A' and resid 449 through 458 removed outlier: 3.953A pdb=" N TYR A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TYR A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N TYR A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 4.153A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.887A 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: 3.522A pdb=" N LEU A 527 " --> pdb=" O ASP A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 579 removed outlier: 4.110A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.821A 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 641 removed outlier: 4.848A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 661 Processing helix chain 'A' and resid 688 through 709 Processing helix chain 'A' and resid 718 through 732 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 857 through 871 Proline residue: A 868 - end of helix removed outlier: 4.696A pdb=" N LYS A 871 " --> pdb=" O TYR A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 902 removed outlier: 3.986A 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: 3.923A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 915 Processing helix chain 'A' and resid 919 through 925 removed outlier: 3.971A pdb=" N MET A 924 " --> pdb=" O PHE A 920 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR A 925 " --> pdb=" O TYR A 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 32 through 78 removed outlier: 4.047A pdb=" N ALA B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLN B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 96 Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 117 through 124 Proline residue: B 121 - end of helix Processing helix chain 'B' and resid 135 through 142 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: 3.653A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.588A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 61 removed outlier: 3.712A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 Processing helix chain 'D' and resid 10 through 28 Processing helix chain 'D' and resid 33 through 81 removed outlier: 3.570A pdb=" N GLN D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 101 through 112 Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.579A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) 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 105 through 111 Processing helix chain 'E' and resid 118 through 122 Processing helix chain 'E' and resid 128 through 148 removed outlier: 3.526A pdb=" N ALA E 135 " --> pdb=" O LYS E 131 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N SER E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 274 Processing helix chain 'E' and resid 288 through 298 removed outlier: 3.504A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 324 removed outlier: 3.655A pdb=" N ALA E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) 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 455 removed outlier: 4.556A 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 516 through 525 removed outlier: 4.491A pdb=" N SER E 523 " --> pdb=" O ASN E 519 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 4.464A 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: 4.523A pdb=" N ARG E 567 " --> pdb=" O VAL E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 584 No H-bonds generated for 'chain 'E' and resid 581 through 584' Processing helix chain 'F' and resid 27 through 36 removed outlier: 3.641A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 111 removed outlier: 4.538A pdb=" N ALA F 108 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 128 through 147 removed outlier: 3.755A pdb=" N PHE F 133 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 274 removed outlier: 3.772A pdb=" N VAL F 266 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA F 267 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET F 274 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 298 removed outlier: 4.047A pdb=" N ILE F 293 " --> pdb=" O SER F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 323 Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 381 through 390 Processing helix chain 'F' and resid 419 through 421 No H-bonds generated for 'chain 'F' and resid 419 through 421' Processing helix chain 'F' and resid 424 through 431 Processing helix chain 'F' and resid 446 through 455 Processing helix chain 'F' and resid 490 through 498 Processing helix chain 'F' and resid 516 through 525 removed outlier: 3.515A pdb=" N SER F 523 " --> pdb=" O ASN F 519 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 558 through 565 Processing helix chain 'F' and resid 579 through 583 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 31 through 33 Processing sheet with id= C, first strand: chain 'A' and resid 36 through 38 Processing sheet with id= D, first strand: chain 'A' and resid 98 through 105 removed outlier: 4.315A pdb=" N LYS A 98 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 202 through 204 removed outlier: 6.524A pdb=" N VAL A 231 " --> pdb=" O GLY A 203 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 330 through 335 Processing sheet with id= G, first strand: chain 'A' and resid 345 through 348 Processing sheet with id= H, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.466A pdb=" N MET A 666 " --> pdb=" O THR A 540 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N MET A 542 " --> pdb=" O MET A 666 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N MET A 668 " --> pdb=" O MET A 542 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N LEU A 544 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= J, first strand: chain 'A' and resid 816 through 822 Processing sheet with id= K, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.222A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.244A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= N, first strand: chain 'E' and resid 197 through 199 Processing sheet with id= O, first strand: chain 'E' and resid 277 through 280 removed outlier: 6.609A pdb=" N TYR E 396 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N LEU E 280 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TYR E 398 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE E 399 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE E 373 " --> pdb=" O ILE E 399 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 471 through 475 removed outlier: 6.496A pdb=" N ILE E 572 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N MET E 474 " --> pdb=" O ILE E 572 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N CYS E 574 " --> pdb=" O MET E 474 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER E 513 " --> pdb=" O GLN E 531 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 64 through 66 Processing sheet with id= R, first strand: chain 'F' and resid 197 through 199 Processing sheet with id= S, first strand: chain 'F' and resid 277 through 280 removed outlier: 6.663A pdb=" N TYR F 396 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N LEU F 280 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR F 398 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 308 " --> pdb=" O CYS F 358 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 366 through 368 removed outlier: 3.595A pdb=" N ARG F 392 " --> pdb=" O THR F 366 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 510 through 513 removed outlier: 3.916A pdb=" N THR F 547 " --> pdb=" O ILE F 512 " (cutoff:3.500A) 683 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 8.07 Time building geometry restraints manager: 10.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 9075 1.41 - 1.61: 12879 1.61 - 1.81: 222 1.81 - 2.02: 1 2.02 - 2.22: 1 Bond restraints: 22178 Sorted by residual: bond pdb=" C ALA B 74 " pdb=" N ARG B 75 " ideal model delta sigma weight residual 1.332 2.222 -0.889 1.40e-02 5.10e+03 4.04e+03 bond pdb=" C ALA B 53 " pdb=" N ALA B 54 " ideal model delta sigma weight residual 1.332 1.789 -0.457 1.40e-02 5.10e+03 1.06e+03 bond pdb=" C PRO F 234 " pdb=" N LEU F 235 " ideal model delta sigma weight residual 1.329 1.621 -0.292 1.43e-02 4.89e+03 4.17e+02 bond pdb=" F1 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.70e+01 bond pdb=" F2 AF3 F1005 " pdb="AL AF3 F1005 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 22173 not shown) Histogram of bond angle deviations from ideal: 63.04 - 78.39: 1 78.39 - 93.73: 0 93.73 - 109.07: 2406 109.07 - 124.41: 27472 124.41 - 139.75: 599 Bond angle restraints: 30478 Sorted by residual: angle pdb=" O ALA B 53 " pdb=" C ALA B 53 " pdb=" N ALA B 54 " ideal model delta sigma weight residual 122.59 63.04 59.55 1.33e+00 5.65e-01 2.00e+03 angle pdb=" O PRO F 234 " pdb=" C PRO F 234 " pdb=" N LEU F 235 " ideal model delta sigma weight residual 123.10 106.18 16.92 1.20e+00 6.94e-01 1.99e+02 angle pdb=" CA PRO F 234 " pdb=" C PRO F 234 " pdb=" N LEU F 235 " ideal model delta sigma weight residual 115.50 130.25 -14.75 1.27e+00 6.20e-01 1.35e+02 angle pdb=" C PRO F 234 " pdb=" N LEU F 235 " pdb=" CA LEU F 235 " ideal model delta sigma weight residual 122.65 139.75 -17.10 1.49e+00 4.50e-01 1.32e+02 angle pdb=" CA ALA B 53 " pdb=" C ALA B 53 " pdb=" N ALA B 54 " ideal model delta sigma weight residual 116.84 135.68 -18.84 1.71e+00 3.42e-01 1.21e+02 ... (remaining 30473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 12881 34.00 - 68.01: 446 68.01 - 102.01: 30 102.01 - 136.02: 6 136.02 - 170.02: 3 Dihedral angle restraints: 13366 sinusoidal: 5811 harmonic: 7555 Sorted by residual: dihedral pdb=" CA SER E 80 " pdb=" C SER E 80 " pdb=" N PHE E 81 " pdb=" CA PHE E 81 " ideal model delta harmonic sigma weight residual 180.00 48.83 131.17 0 5.00e+00 4.00e-02 6.88e+02 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 42.52 -42.52 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CA ASN F 190 " pdb=" C ASN F 190 " pdb=" N SER F 191 " pdb=" CA SER F 191 " ideal model delta harmonic sigma weight residual 180.00 139.31 40.69 0 5.00e+00 4.00e-02 6.62e+01 ... (remaining 13363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3008 0.062 - 0.123: 472 0.123 - 0.185: 47 0.185 - 0.247: 6 0.247 - 0.308: 3 Chirality restraints: 3536 Sorted by residual: chirality pdb=" CA TYR F 149 " pdb=" N TYR F 149 " pdb=" C TYR F 149 " pdb=" CB TYR F 149 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA VAL E 2 " pdb=" N VAL E 2 " pdb=" C VAL E 2 " pdb=" CB VAL E 2 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASN F 190 " pdb=" N ASN F 190 " pdb=" C ASN F 190 " pdb=" CB ASN F 190 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 3533 not shown) Planarity restraints: 3617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 53 " 0.174 2.00e-02 2.50e+03 2.20e-01 4.83e+02 pdb=" C ALA B 53 " -0.377 2.00e-02 2.50e+03 pdb=" O ALA B 53 " 0.100 2.00e-02 2.50e+03 pdb=" N ALA B 54 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 74 " -0.088 2.00e-02 2.50e+03 1.45e-01 2.10e+02 pdb=" C ALA B 74 " 0.248 2.00e-02 2.50e+03 pdb=" O ALA B 74 " -0.108 2.00e-02 2.50e+03 pdb=" N ARG B 75 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET E 233 " 0.077 5.00e-02 4.00e+02 1.17e-01 2.20e+01 pdb=" N PRO E 234 " -0.203 5.00e-02 4.00e+02 pdb=" CA PRO E 234 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 234 " 0.062 5.00e-02 4.00e+02 ... (remaining 3614 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 12 1.88 - 2.64: 422 2.64 - 3.39: 28978 3.39 - 4.15: 53905 4.15 - 4.90: 96294 Nonbonded interactions: 179611 Sorted by model distance: nonbonded pdb=" O ASP E 101 " pdb=" N VAL E 103 " model vdw 1.129 2.520 nonbonded pdb=" CG2 THR E 214 " pdb=" NH1 ARG E 337 " model vdw 1.208 3.540 nonbonded pdb=" O ASP F 204 " pdb=" CE LYS F 524 " model vdw 1.226 3.440 nonbonded pdb=" NZ LYS B 61 " pdb=" OP1 G T 113 " model vdw 1.429 2.520 nonbonded pdb=" O ASP F 101 " pdb=" N VAL F 103 " model vdw 1.432 2.520 ... (remaining 179606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 7 through 22 or (resid 23 through 25 and (name N or name C \ A or name C or name O or name CB )) or resid 26 through 191)) selection = (chain 'D' and (resid 7 through 31 or (resid 32 and (name N or name CA or name C \ or name O or name CB )) or resid 33 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and (n \ ame N or name CA or name C or name O or name CB )) or resid 40 through 47 or (re \ sid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thro \ ugh 191)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.790 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 67.440 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 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 : 0.009 0.889 22178 Z= 0.675 Angle : 0.882 59.546 30478 Z= 0.544 Chirality : 0.046 0.308 3536 Planarity : 0.007 0.220 3617 Dihedral : 16.126 170.022 8492 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.66 % Favored : 93.15 % Rotamer: Outliers : 9.24 % Allowed : 9.11 % Favored : 81.65 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.16), residues: 2539 helix: -0.60 (0.16), residues: 1004 sheet: -1.02 (0.29), residues: 299 loop : -1.71 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 916 HIS 0.012 0.001 HIS F 290 PHE 0.019 0.002 PHE A 102 TYR 0.020 0.002 TYR F 224 ARG 0.005 0.001 ARG F 443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5078 Ramachandran restraints generated. 2539 Oldfield, 0 Emsley, 2539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 241 time to evaluate : 2.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8228 (t) cc_final: 0.7942 (m) REVERT: A 758 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8815 (tt) REVERT: A 761 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: B 15 PHE cc_start: 0.8373 (t80) cc_final: 0.7768 (t80) REVERT: B 94 MET cc_start: 0.8404 (mtm) cc_final: 0.8190 (mtt) REVERT: D 42 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8288 (tp) REVERT: D 48 GLU cc_start: 0.9093 (tp30) cc_final: 0.8883 (tp30) REVERT: E 204 ASP cc_start: 0.3220 (OUTLIER) cc_final: 0.1975 (t0) REVERT: E 441 CYS cc_start: 0.2933 (OUTLIER) cc_final: 0.2605 (t) REVERT: E 548 GLN cc_start: -0.0621 (OUTLIER) cc_final: -0.0848 (tt0) REVERT: F 210 VAL cc_start: 0.4201 (OUTLIER) cc_final: 0.3574 (m) REVERT: F 258 ILE cc_start: -0.0112 (OUTLIER) cc_final: -0.0494 (tt) REVERT: F 376 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7100 (mp) REVERT: F 455 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6124 (tp) outliers start: 203 outliers final: 43 residues processed: 426 average time/residue: 0.3210 time to fit residues: 209.3810 Evaluate side-chains 180 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 127 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 441 CYS Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 548 GLN Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 585 LEU Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 218 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 108 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 151 optimal weight: 30.0000 chunk 235 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 ASN C 19 GLN E 537 GLN F 354 GLN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22178 Z= 0.244 Angle : 0.659 14.593 30478 Z= 0.334 Chirality : 0.043 0.287 3536 Planarity : 0.004 0.047 3617 Dihedral : 14.409 179.857 3999 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.12 % Favored : 94.81 % Rotamer: Outliers : 4.87 % Allowed : 14.85 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.16), residues: 2541 helix: -0.00 (0.16), residues: 986 sheet: -0.69 (0.31), residues: 274 loop : -1.53 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 916 HIS 0.008 0.001 HIS E 290 PHE 0.025 0.002 PHE B 15 TYR 0.020 0.002 TYR B 71 ARG 0.015 0.001 ARG E 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 134 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 VAL cc_start: 0.8451 (t) cc_final: 0.8230 (m) REVERT: A 242 MET cc_start: 0.8277 (mtt) cc_final: 0.8025 (mtt) REVERT: A 903 TYR cc_start: 0.6907 (m-80) cc_final: 0.6240 (m-80) REVERT: B 65 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8139 (mm-40) REVERT: C 47 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7174 (tm-30) REVERT: D 60 GLU cc_start: 0.8438 (pp20) cc_final: 0.8236 (pp20) REVERT: E 204 ASP cc_start: 0.3327 (OUTLIER) cc_final: 0.1840 (t0) REVERT: F 258 ILE cc_start: 0.0498 (OUTLIER) cc_final: 0.0185 (tt) outliers start: 107 outliers final: 52 residues processed: 234 average time/residue: 0.3196 time to fit residues: 118.8597 Evaluate side-chains 169 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 114 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 130 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 160 optimal weight: 0.0770 chunk 64 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 254 optimal weight: 10.0000 chunk 209 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 572 HIS ** A 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 791 ASN D 43 ASN D 157 GLN D 168 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN E 554 HIS E 562 ASN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 22178 Z= 0.444 Angle : 0.708 14.507 30478 Z= 0.364 Chirality : 0.044 0.233 3536 Planarity : 0.004 0.041 3617 Dihedral : 13.847 149.349 3957 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.69 % Allowed : 15.76 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.16), residues: 2541 helix: 0.05 (0.16), residues: 1015 sheet: -0.65 (0.32), residues: 269 loop : -1.47 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 114 HIS 0.014 0.002 HIS F 164 PHE 0.020 0.002 PHE D 92 TYR 0.019 0.002 TYR A 887 ARG 0.005 0.001 ARG F 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 117 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8101 (mmm) cc_final: 0.7712 (mmp) REVERT: A 132 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8722 (mtp180) REVERT: A 153 ASP cc_start: 0.7245 (p0) cc_final: 0.7026 (p0) REVERT: A 924 MET cc_start: 0.9163 (mmm) cc_final: 0.8858 (mmt) REVERT: C 47 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7706 (tm-30) REVERT: D 48 GLU cc_start: 0.9147 (tp30) cc_final: 0.7904 (tp30) REVERT: D 52 ASP cc_start: 0.8740 (m-30) cc_final: 0.7745 (m-30) REVERT: E 204 ASP cc_start: 0.3170 (OUTLIER) cc_final: 0.1832 (t0) REVERT: E 327 ILE cc_start: 0.2525 (OUTLIER) cc_final: 0.2131 (mm) REVERT: E 429 MET cc_start: 0.5331 (tpp) cc_final: 0.4932 (tpp) REVERT: F 26 CYS cc_start: 0.6393 (OUTLIER) cc_final: 0.6001 (p) REVERT: F 258 ILE cc_start: 0.0485 (OUTLIER) cc_final: 0.0151 (tt) REVERT: F 474 MET cc_start: 0.7416 (mpp) cc_final: 0.7031 (tpt) outliers start: 103 outliers final: 63 residues processed: 210 average time/residue: 0.3270 time to fit residues: 107.1759 Evaluate side-chains 178 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 110 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 459 ASN Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 525 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 232 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 26 optimal weight: 0.0970 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 224 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22178 Z= 0.242 Angle : 0.596 14.325 30478 Z= 0.301 Chirality : 0.041 0.248 3536 Planarity : 0.003 0.040 3617 Dihedral : 13.626 145.265 3951 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.64 % Allowed : 17.62 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2541 helix: 0.43 (0.16), residues: 1007 sheet: -0.20 (0.33), residues: 253 loop : -1.35 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 114 HIS 0.006 0.001 HIS E 290 PHE 0.015 0.001 PHE D 92 TYR 0.017 0.001 TYR E 277 ARG 0.009 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 117 time to evaluate : 2.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.8222 (tmm) cc_final: 0.7654 (ttt) REVERT: A 924 MET cc_start: 0.9105 (mmm) cc_final: 0.8651 (mmt) REVERT: C 47 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7587 (tm-30) REVERT: D 48 GLU cc_start: 0.9115 (tp30) cc_final: 0.8031 (tp30) REVERT: D 52 ASP cc_start: 0.8678 (m-30) cc_final: 0.8121 (m-30) REVERT: D 60 GLU cc_start: 0.8486 (pp20) cc_final: 0.8268 (pp20) REVERT: D 94 MET cc_start: 0.8549 (mtm) cc_final: 0.8112 (mtp) REVERT: D 185 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8231 (mp) REVERT: E 204 ASP cc_start: 0.3120 (OUTLIER) cc_final: 0.1867 (t0) REVERT: E 324 TYR cc_start: 0.2840 (m-10) cc_final: 0.2525 (m-10) REVERT: E 429 MET cc_start: 0.4884 (tpp) cc_final: 0.4577 (tpp) REVERT: E 493 ILE cc_start: 0.4072 (OUTLIER) cc_final: 0.3665 (pt) REVERT: F 26 CYS cc_start: 0.6516 (OUTLIER) cc_final: 0.6053 (p) REVERT: F 258 ILE cc_start: 0.0578 (OUTLIER) cc_final: 0.0242 (tt) outliers start: 80 outliers final: 54 residues processed: 191 average time/residue: 0.3134 time to fit residues: 95.8521 Evaluate side-chains 171 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 112 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 70 TYR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 208 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 186 optimal weight: 6.9990 chunk 103 optimal weight: 0.1980 chunk 213 optimal weight: 20.0000 chunk 173 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 HIS ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22178 Z= 0.183 Angle : 0.566 14.226 30478 Z= 0.284 Chirality : 0.039 0.213 3536 Planarity : 0.003 0.041 3617 Dihedral : 13.405 147.229 3942 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.55 % Allowed : 17.85 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 2541 helix: 0.63 (0.17), residues: 1011 sheet: -0.23 (0.33), residues: 259 loop : -1.23 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.006 0.001 HIS E 164 PHE 0.014 0.001 PHE B 15 TYR 0.015 0.001 TYR F 224 ARG 0.005 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 120 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.7936 (mmm) cc_final: 0.7692 (mmm) REVERT: A 132 ARG cc_start: 0.8949 (OUTLIER) cc_final: 0.8674 (mtp180) REVERT: A 268 TRP cc_start: 0.8614 (OUTLIER) cc_final: 0.7170 (m-90) REVERT: A 615 MET cc_start: 0.8166 (tmm) cc_final: 0.7709 (ttm) REVERT: B 94 MET cc_start: 0.8384 (mtp) cc_final: 0.8021 (mtp) REVERT: C 47 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7527 (tm-30) REVERT: D 48 GLU cc_start: 0.9070 (tp30) cc_final: 0.7958 (tp30) REVERT: D 52 ASP cc_start: 0.8688 (m-30) cc_final: 0.8117 (m-30) REVERT: D 60 GLU cc_start: 0.8472 (pp20) cc_final: 0.8222 (pp20) REVERT: D 185 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8219 (mp) REVERT: E 68 MET cc_start: 0.7654 (mmm) cc_final: 0.6451 (mmm) REVERT: E 204 ASP cc_start: 0.3127 (OUTLIER) cc_final: 0.1897 (t0) REVERT: E 324 TYR cc_start: 0.3021 (m-10) cc_final: 0.2719 (m-10) REVERT: E 429 MET cc_start: 0.4869 (tpp) cc_final: 0.4560 (tpp) REVERT: F 26 CYS cc_start: 0.6377 (OUTLIER) cc_final: 0.5905 (p) REVERT: F 258 ILE cc_start: 0.1180 (OUTLIER) cc_final: 0.0846 (tt) REVERT: F 328 ASP cc_start: 0.6807 (p0) cc_final: 0.6577 (p0) REVERT: F 474 MET cc_start: 0.7038 (mpp) cc_final: 0.6653 (tpt) outliers start: 78 outliers final: 54 residues processed: 187 average time/residue: 0.3117 time to fit residues: 93.2815 Evaluate side-chains 172 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 112 time to evaluate : 2.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 493 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 84 optimal weight: 3.9990 chunk 225 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 250 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 116 optimal weight: 0.0270 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22178 Z= 0.162 Angle : 0.566 14.155 30478 Z= 0.279 Chirality : 0.039 0.208 3536 Planarity : 0.003 0.040 3617 Dihedral : 13.252 148.272 3931 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.10 % Allowed : 18.67 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.17), residues: 2541 helix: 0.84 (0.17), residues: 998 sheet: -0.03 (0.34), residues: 240 loop : -1.14 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS E 290 PHE 0.013 0.001 PHE D 92 TYR 0.015 0.001 TYR F 224 ARG 0.003 0.000 ARG B 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 120 time to evaluate : 2.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8570 (mtp180) REVERT: A 268 TRP cc_start: 0.8591 (OUTLIER) cc_final: 0.7116 (m-90) REVERT: A 566 MET cc_start: 0.8369 (ttm) cc_final: 0.8160 (mtp) REVERT: A 615 MET cc_start: 0.8099 (tmm) cc_final: 0.7673 (ttm) REVERT: B 15 PHE cc_start: 0.8326 (t80) cc_final: 0.8002 (t80) REVERT: B 94 MET cc_start: 0.8391 (mtp) cc_final: 0.8071 (mtp) REVERT: C 47 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7471 (tm-30) REVERT: C 74 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7485 (mp0) REVERT: D 48 GLU cc_start: 0.9034 (tp30) cc_final: 0.7876 (tp30) REVERT: D 52 ASP cc_start: 0.8679 (m-30) cc_final: 0.8101 (m-30) REVERT: D 185 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8214 (mp) REVERT: E 204 ASP cc_start: 0.3280 (OUTLIER) cc_final: 0.2134 (t0) REVERT: E 324 TYR cc_start: 0.3034 (m-10) cc_final: 0.2724 (m-10) REVERT: E 429 MET cc_start: 0.4807 (tpp) cc_final: 0.4518 (tpp) REVERT: F 26 CYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5883 (p) REVERT: F 258 ILE cc_start: 0.1172 (OUTLIER) cc_final: 0.0841 (tt) REVERT: F 328 ASP cc_start: 0.7069 (p0) cc_final: 0.6828 (p0) REVERT: F 474 MET cc_start: 0.6802 (mpp) cc_final: 0.6454 (tpt) outliers start: 68 outliers final: 55 residues processed: 180 average time/residue: 0.3040 time to fit residues: 88.0495 Evaluate side-chains 173 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 112 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 241 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 210 optimal weight: 10.0000 chunk 139 optimal weight: 9.9990 chunk 249 optimal weight: 8.9990 chunk 156 optimal weight: 30.0000 chunk 152 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 705 ASN B 19 GLN C 63 GLN E 164 HIS ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 22178 Z= 0.502 Angle : 0.725 14.077 30478 Z= 0.367 Chirality : 0.045 0.218 3536 Planarity : 0.004 0.037 3617 Dihedral : 13.402 148.627 3931 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.01 % Allowed : 17.94 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2541 helix: 0.50 (0.16), residues: 1000 sheet: -0.61 (0.33), residues: 259 loop : -1.28 (0.17), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 114 HIS 0.009 0.001 HIS C 36 PHE 0.023 0.002 PHE D 92 TYR 0.024 0.002 TYR A 887 ARG 0.006 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 106 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8776 (mtp180) REVERT: A 268 TRP cc_start: 0.8679 (OUTLIER) cc_final: 0.7285 (m-90) REVERT: B 94 MET cc_start: 0.8548 (mtp) cc_final: 0.8167 (mtp) REVERT: C 3 MET cc_start: 0.8871 (tpp) cc_final: 0.8526 (tpp) REVERT: C 47 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7922 (tm-30) REVERT: D 48 GLU cc_start: 0.9053 (tp30) cc_final: 0.8640 (tp30) REVERT: D 185 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8330 (mp) REVERT: E 204 ASP cc_start: 0.3617 (OUTLIER) cc_final: 0.2407 (t0) REVERT: E 324 TYR cc_start: 0.3383 (m-10) cc_final: 0.2802 (m-10) REVERT: E 429 MET cc_start: 0.5375 (tpp) cc_final: 0.5127 (tpp) REVERT: F 26 CYS cc_start: 0.6570 (OUTLIER) cc_final: 0.6156 (p) REVERT: F 474 MET cc_start: 0.6963 (mpp) cc_final: 0.6654 (tpt) outliers start: 88 outliers final: 61 residues processed: 185 average time/residue: 0.3111 time to fit residues: 92.5768 Evaluate side-chains 166 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 100 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 761 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 378 MET Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 552 THR Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 154 optimal weight: 50.0000 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 196 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22178 Z= 0.236 Angle : 0.601 14.080 30478 Z= 0.299 Chirality : 0.040 0.205 3536 Planarity : 0.003 0.039 3617 Dihedral : 13.314 149.045 3927 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.51 % Allowed : 18.90 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2541 helix: 0.74 (0.17), residues: 994 sheet: -0.54 (0.33), residues: 260 loop : -1.15 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 916 HIS 0.005 0.001 HIS F 164 PHE 0.017 0.001 PHE D 92 TYR 0.016 0.001 TYR F 224 ARG 0.005 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 112 time to evaluate : 2.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 MET cc_start: 0.8035 (mmm) cc_final: 0.7801 (tpt) REVERT: A 268 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.7151 (m-90) REVERT: A 615 MET cc_start: 0.8186 (tmm) cc_final: 0.7679 (ttm) REVERT: A 665 GLU cc_start: 0.7299 (pm20) cc_final: 0.7050 (pm20) REVERT: B 94 MET cc_start: 0.8402 (mtp) cc_final: 0.7881 (mtp) REVERT: C 3 MET cc_start: 0.8701 (tpp) cc_final: 0.8419 (tpp) REVERT: C 47 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7762 (tm-30) REVERT: D 48 GLU cc_start: 0.9020 (tp30) cc_final: 0.8654 (tp30) REVERT: D 94 MET cc_start: 0.8511 (mtp) cc_final: 0.8270 (mtp) REVERT: D 185 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8247 (mp) REVERT: E 204 ASP cc_start: 0.3550 (OUTLIER) cc_final: 0.2521 (t0) REVERT: E 378 MET cc_start: 0.3871 (OUTLIER) cc_final: 0.3597 (ptt) REVERT: F 26 CYS cc_start: 0.6636 (OUTLIER) cc_final: 0.6145 (p) outliers start: 77 outliers final: 59 residues processed: 180 average time/residue: 0.3143 time to fit residues: 91.6168 Evaluate side-chains 167 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 103 time to evaluate : 2.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 378 MET Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 436 MET Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 166 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 483 ASP Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 573 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 227 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 218 optimal weight: 8.9990 chunk 232 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 210 optimal weight: 40.0000 chunk 220 optimal weight: 0.0770 chunk 231 optimal weight: 10.0000 overall best weight: 2.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 19 GLN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22178 Z= 0.311 Angle : 0.625 13.956 30478 Z= 0.312 Chirality : 0.041 0.206 3536 Planarity : 0.003 0.040 3617 Dihedral : 13.169 150.538 3927 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.23 % Allowed : 19.35 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2541 helix: 0.80 (0.17), residues: 988 sheet: -0.82 (0.32), residues: 283 loop : -1.13 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 506 HIS 0.006 0.001 HIS E 290 PHE 0.018 0.002 PHE D 92 TYR 0.016 0.001 TYR F 224 ARG 0.005 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 109 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 TRP cc_start: 0.8645 (OUTLIER) cc_final: 0.7161 (m-90) REVERT: A 615 MET cc_start: 0.8233 (tmm) cc_final: 0.7720 (ttm) REVERT: A 665 GLU cc_start: 0.7258 (pm20) cc_final: 0.7002 (pm20) REVERT: A 666 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8072 (mtm) REVERT: A 924 MET cc_start: 0.8754 (mmm) cc_final: 0.8419 (mtp) REVERT: B 94 MET cc_start: 0.8219 (mtp) cc_final: 0.7854 (mtp) REVERT: C 3 MET cc_start: 0.8827 (tpp) cc_final: 0.8540 (tpp) REVERT: D 48 GLU cc_start: 0.8955 (tp30) cc_final: 0.8538 (tp30) REVERT: D 185 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8306 (mp) REVERT: E 378 MET cc_start: 0.3912 (OUTLIER) cc_final: 0.3620 (ptt) REVERT: F 26 CYS cc_start: 0.6577 (OUTLIER) cc_final: 0.6121 (p) outliers start: 71 outliers final: 59 residues processed: 174 average time/residue: 0.2983 time to fit residues: 85.0818 Evaluate side-chains 166 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 102 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 386 ASN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 378 MET Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 410 THR Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 177 ASN Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 588 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 152 optimal weight: 0.5980 chunk 245 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 205 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 158 optimal weight: 0.4980 chunk 125 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22178 Z= 0.189 Angle : 0.582 13.906 30478 Z= 0.287 Chirality : 0.040 0.197 3536 Planarity : 0.003 0.041 3617 Dihedral : 13.090 151.311 3924 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.69 % Allowed : 19.81 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2541 helix: 0.88 (0.17), residues: 993 sheet: -0.61 (0.32), residues: 268 loop : -1.05 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS F 164 PHE 0.016 0.001 PHE B 15 TYR 0.017 0.001 TYR F 224 ARG 0.004 0.000 ARG A 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5082 Ramachandran restraints generated. 2541 Oldfield, 0 Emsley, 2541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 109 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 TRP cc_start: 0.8591 (OUTLIER) cc_final: 0.7115 (m-90) REVERT: A 615 MET cc_start: 0.8147 (tmm) cc_final: 0.7749 (ttm) REVERT: A 665 GLU cc_start: 0.7175 (pm20) cc_final: 0.6947 (pm20) REVERT: A 924 MET cc_start: 0.8803 (mmm) cc_final: 0.8492 (mtp) REVERT: C 3 MET cc_start: 0.8675 (tpp) cc_final: 0.8424 (tpp) REVERT: C 34 GLN cc_start: 0.8239 (tp40) cc_final: 0.7943 (tm-30) REVERT: C 47 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7561 (tm-30) REVERT: D 48 GLU cc_start: 0.8924 (tp30) cc_final: 0.8531 (tp30) REVERT: D 185 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8185 (mp) REVERT: E 219 LEU cc_start: -0.0838 (OUTLIER) cc_final: -0.1189 (mp) REVERT: F 26 CYS cc_start: 0.6482 (OUTLIER) cc_final: 0.5964 (p) outliers start: 59 outliers final: 52 residues processed: 163 average time/residue: 0.3067 time to fit residues: 81.5021 Evaluate side-chains 159 residues out of total 2230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 103 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 109 ASP Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 268 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 44 ASP Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 265 ASN Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain E residue 370 ILE Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 519 ASN Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 561 PHE Chi-restraints excluded: chain E residue 572 ILE Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 26 CYS Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 187 VAL Chi-restraints excluded: chain F residue 209 VAL Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 226 VAL Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 357 PHE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 370 ILE Chi-restraints excluded: chain F residue 391 LEU Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 438 LEU Chi-restraints excluded: chain F residue 499 PHE Chi-restraints excluded: chain F residue 506 TRP Chi-restraints excluded: chain F residue 507 ARG Chi-restraints excluded: chain F residue 525 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: chunk 163 optimal weight: 0.0980 chunk 218 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 205 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 211 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.087953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.058010 restraints weight = 92788.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.059993 restraints weight = 38497.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.061211 restraints weight = 22129.067| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22178 Z= 0.172 Angle : 0.566 13.821 30478 Z= 0.279 Chirality : 0.039 0.209 3536 Planarity : 0.003 0.042 3617 Dihedral : 12.981 152.499 3923 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.69 % Allowed : 19.72 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2541 helix: 1.00 (0.17), residues: 986 sheet: -0.62 (0.33), residues: 266 loop : -1.00 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS F 164 PHE 0.015 0.001 PHE B 15 TYR 0.015 0.001 TYR F 224 ARG 0.003 0.000 ARG A 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3779.37 seconds wall clock time: 70 minutes 4.10 seconds (4204.10 seconds total)