Starting phenix.real_space_refine on Sun Mar 24 12:22:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4c_17405/03_2024/8p4c_17405.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4c_17405/03_2024/8p4c_17405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4c_17405/03_2024/8p4c_17405.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4c_17405/03_2024/8p4c_17405.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4c_17405/03_2024/8p4c_17405.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p4c_17405/03_2024/8p4c_17405.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.005 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 90 5.49 5 Mg 1 5.21 5 S 248 5.16 5 C 25912 2.51 5 N 7276 2.21 5 O 7909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 146": "OD1" <-> "OD2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 631": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 763": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 813": "OD1" <-> "OD2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A ASP 876": "OD1" <-> "OD2" Residue "A TYR 924": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 957": "OE1" <-> "OE2" Residue "A GLU 961": "OE1" <-> "OE2" Residue "A TYR 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1349": "OE1" <-> "OE2" Residue "A GLU 1381": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "M GLU 82": "OE1" <-> "OE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M GLU 101": "OE1" <-> "OE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "M PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 115": "OE1" <-> "OE2" Residue "M GLU 120": "OE1" <-> "OE2" Residue "M GLU 143": "OE1" <-> "OE2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 172": "OE1" <-> "OE2" Residue "M PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 277": "OD1" <-> "OD2" Residue "M ASP 296": "OD1" <-> "OD2" Residue "M TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 309": "OE1" <-> "OE2" Residue "M PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 332": "OD1" <-> "OD2" Residue "M ASP 343": "OD1" <-> "OD2" Residue "M TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 363": "OD1" <-> "OD2" Residue "M ASP 374": "OD1" <-> "OD2" Residue "M PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 532": "OD1" <-> "OD2" Residue "M PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 383": "OD1" <-> "OD2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B ASP 792": "OD1" <-> "OD2" Residue "B TYR 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1161": "OE1" <-> "OE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "F GLU 86": "OE1" <-> "OE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F ASP 112": "OD1" <-> "OD2" Residue "F ASP 117": "OD1" <-> "OD2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 19": "OE1" <-> "OE2" Residue "I TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 43": "OD1" <-> "OD2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 63": "OD1" <-> "OD2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I ASP 75": "OD1" <-> "OD2" Residue "I PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 54": "OD1" <-> "OD2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K ASP 39": "OD1" <-> "OD2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 103": "OE1" <-> "OE2" Residue "K ASP 111": "OD1" <-> "OD2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "L ASP 32": "OD1" <-> "OD2" Residue "L ASP 56": "OD1" <-> "OD2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 132": "OD1" <-> "OD2" Residue "G TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 198": "NH1" <-> "NH2" Residue "Z ARG 555": "NH1" <-> "NH2" Residue "Z ARG 571": "NH1" <-> "NH2" Residue "Z ARG 577": "NH1" <-> "NH2" Residue "Z ARG 582": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41439 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11166 Classifications: {'peptide': 1410} Link IDs: {'PCIS': 1, 'PTRANS': 68, 'TRANS': 1340} Chain breaks: 5 Chain: "M" Number of atoms: 3958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3958 Classifications: {'peptide': 493} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 466} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain breaks: 1 Chain: "T" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 847 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "B" Number of atoms: 9052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1132, 9052 Classifications: {'peptide': 1132} Link IDs: {'PTRANS': 53, 'TRANS': 1078} Chain breaks: 4 Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2115 Classifications: {'peptide': 263} Link IDs: {'PTRANS': 15, 'TRANS': 247} Chain breaks: 1 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 949 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "J" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 533 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 388 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "P" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 368 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 9, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 13} Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 3676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3676 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 17, 'TRANS': 440} Chain breaks: 7 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 464 SG CYS A 71 67.597 106.007 96.878 1.00 99.80 S ATOM 486 SG CYS A 74 71.539 106.013 96.131 1.00 95.82 S ATOM 768 SG CYS A 111 81.212 116.736 141.941 1.00132.71 S ATOM 796 SG CYS A 114 80.810 118.329 140.849 1.00130.87 S ATOM 36967 SG CYS Y 16 24.446 129.179 133.123 1.00 81.24 S ATOM 36989 SG CYS Y 19 25.411 127.429 136.957 1.00 84.47 S ATOM 37101 SG CYS Y 33 21.711 127.569 136.314 1.00 73.71 S Time building chain proxies: 20.53, per 1000 atoms: 0.50 Number of scatterers: 41439 At special positions: 0 Unit cell: (158.55, 166.95, 202.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 248 16.00 P 90 15.00 Mg 1 11.99 O 7909 8.00 N 7276 7.00 C 25912 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 Atom "ATOM 15309 O5' DA N 24 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.83 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 16 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 33 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9304 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 57 sheets defined 34.8% alpha, 18.5% beta 39 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 13.29 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 136 through 149 Processing helix chain 'A' and resid 217 through 227 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 274 through 297 Processing helix chain 'A' and resid 301 through 319 removed outlier: 3.605A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 334 removed outlier: 4.008A pdb=" N ARG A 334 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 381 through 386 Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 488 through 493 removed outlier: 3.616A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.860A pdb=" N ILE A 525 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 549 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.857A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 616 removed outlier: 4.285A pdb=" N SER A 615 " --> pdb=" O ASP A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.534A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 Processing helix chain 'A' and resid 696 through 722 removed outlier: 3.687A pdb=" N GLN A 700 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 760 Processing helix chain 'A' and resid 764 through 771 Processing helix chain 'A' and resid 777 through 786 removed outlier: 3.732A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 869 removed outlier: 3.539A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A 856 " --> pdb=" O VAL A 852 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 921 removed outlier: 3.520A pdb=" N GLU A 917 " --> pdb=" O ASN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 932 removed outlier: 3.736A pdb=" N LEU A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.664A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 Processing helix chain 'A' and resid 982 through 994 Processing helix chain 'A' and resid 1005 through 1020 removed outlier: 3.690A pdb=" N GLU A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1038 through 1049 Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1061 through 1078 removed outlier: 3.539A pdb=" N GLU A1073 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A1074 " --> pdb=" O GLY A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1150 through 1162 removed outlier: 3.630A pdb=" N ALA A1154 " --> pdb=" O ASP A1150 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 removed outlier: 4.103A pdb=" N VAL A1169 " --> pdb=" O THR A1165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1165 through 1169' Processing helix chain 'A' and resid 1188 through 1195 Processing helix chain 'A' and resid 1217 through 1225 Processing helix chain 'A' and resid 1227 through 1240 Processing helix chain 'A' and resid 1282 through 1295 Processing helix chain 'A' and resid 1361 through 1369 Processing helix chain 'A' and resid 1370 through 1389 removed outlier: 3.560A pdb=" N VAL A1385 " --> pdb=" O GLU A1381 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A1386 " --> pdb=" O LEU A1382 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1405 removed outlier: 3.849A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 Processing helix chain 'A' and resid 1436 through 1446 Processing helix chain 'A' and resid 1454 through 1460 removed outlier: 3.749A pdb=" N MET A1459 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A1460 " --> pdb=" O GLU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1481 removed outlier: 3.526A pdb=" N LYS A1481 " --> pdb=" O ALA A1477 " (cutoff:3.500A) Processing helix chain 'M' and resid 32 through 36 Processing helix chain 'M' and resid 40 through 44 Processing helix chain 'M' and resid 46 through 57 removed outlier: 3.676A pdb=" N LEU M 50 " --> pdb=" O HIS M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 81 Processing helix chain 'M' and resid 99 through 117 removed outlier: 3.791A pdb=" N ARG M 116 " --> pdb=" O ARG M 112 " (cutoff:3.500A) Processing helix chain 'M' and resid 130 through 146 Processing helix chain 'M' and resid 148 through 160 Processing helix chain 'M' and resid 166 through 178 Processing helix chain 'M' and resid 246 through 262 removed outlier: 3.860A pdb=" N GLU M 252 " --> pdb=" O PRO M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 279 through 281 No H-bonds generated for 'chain 'M' and resid 279 through 281' Processing helix chain 'M' and resid 282 through 287 removed outlier: 3.595A pdb=" N LEU M 286 " --> pdb=" O LYS M 282 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS M 287 " --> pdb=" O LEU M 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 282 through 287' Processing helix chain 'M' and resid 371 through 375 Processing helix chain 'M' and resid 376 through 388 Processing helix chain 'M' and resid 388 through 398 removed outlier: 3.671A pdb=" N ARG M 392 " --> pdb=" O ILE M 388 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR M 398 " --> pdb=" O GLU M 394 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 406 removed outlier: 3.588A pdb=" N GLU M 406 " --> pdb=" O LYS M 403 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 424 removed outlier: 3.860A pdb=" N ARG M 422 " --> pdb=" O ILE M 418 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LYS M 423 " --> pdb=" O CYS M 419 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU M 424 " --> pdb=" O THR M 420 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 418 through 424' Processing helix chain 'M' and resid 504 through 508 Processing helix chain 'M' and resid 538 through 551 Processing helix chain 'M' and resid 554 through 564 removed outlier: 3.829A pdb=" N GLU M 560 " --> pdb=" O GLU M 556 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE M 561 " --> pdb=" O MET M 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 37 removed outlier: 4.464A pdb=" N TRP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 5.427A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 269 through 277 Processing helix chain 'B' and resid 281 through 287 removed outlier: 3.534A pdb=" N HIS B 287 " --> pdb=" O ASP B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 306 removed outlier: 3.713A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.526A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.660A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 417 " --> pdb=" O LYS B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 437 through 451 removed outlier: 3.944A pdb=" N SER B 441 " --> pdb=" O THR B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.583A pdb=" N TRP B 506 " --> pdb=" O ASN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 583 through 594 Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.827A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 683 Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 707 through 711 removed outlier: 3.842A pdb=" N ILE B 710 " --> pdb=" O CYS B 707 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 711 " --> pdb=" O ALA B 708 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 707 through 711' Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.643A pdb=" N ASN B 717 " --> pdb=" O PRO B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 729 Processing helix chain 'B' and resid 763 through 768 Processing helix chain 'B' and resid 798 through 804 Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.834A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.529A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 988 " --> pdb=" O CYS B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1017 removed outlier: 3.621A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 27 through 41 removed outlier: 3.646A pdb=" N ILE C 39 " --> pdb=" O ARG C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 77 through 82 removed outlier: 3.664A pdb=" N LYS C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 271 removed outlier: 3.868A pdb=" N VAL C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU C 246 " --> pdb=" O GLU C 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 45 removed outlier: 3.589A pdb=" N PHE E 40 " --> pdb=" O THR E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 removed outlier: 3.889A pdb=" N VAL E 89 " --> pdb=" O LYS E 85 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 Processing helix chain 'E' and resid 133 through 137 removed outlier: 4.253A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.965A pdb=" N LEU E 170 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 removed outlier: 3.534A pdb=" N GLN F 72 " --> pdb=" O THR F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'I' and resid 69 through 75 removed outlier: 3.512A pdb=" N VAL I 72 " --> pdb=" O ILE I 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 26 Processing helix chain 'J' and resid 30 through 38 removed outlier: 3.840A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.794A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 61 removed outlier: 3.545A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 10 removed outlier: 3.717A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 removed outlier: 4.444A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'D' and resid 33 through 50 Processing helix chain 'D' and resid 58 through 71 Processing helix chain 'D' and resid 76 through 90 removed outlier: 3.640A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 removed outlier: 3.759A pdb=" N LEU D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.791A pdb=" N THR G 25 " --> pdb=" O ASN G 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 32 Processing helix chain 'Y' and resid 36 through 41 Processing helix chain 'Y' and resid 45 through 52 removed outlier: 3.642A pdb=" N VAL Y 49 " --> pdb=" O ASN Y 45 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 75 Processing helix chain 'Y' and resid 94 through 104 Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 231 through 239 removed outlier: 3.655A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 245 through 249 removed outlier: 3.563A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) Processing helix chain 'Z' and resid 256 through 260 removed outlier: 3.718A pdb=" N MET Z 260 " --> pdb=" O ILE Z 257 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 349 Processing helix chain 'Z' and resid 464 through 466 No H-bonds generated for 'chain 'Z' and resid 464 through 466' Processing helix chain 'Z' and resid 630 through 633 removed outlier: 4.185A pdb=" N GLY Z 633 " --> pdb=" O VAL Z 630 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 630 through 633' Processing sheet with id=AA1, first strand: chain 'A' and resid 1448 through 1449 removed outlier: 3.690A pdb=" N ARG A 20 " --> pdb=" O MET B1172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 94 removed outlier: 10.669A pdb=" N LEU A 90 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N LYS A 92 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 252 " --> pdb=" O LYS A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 190 through 194 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AA5, first strand: chain 'A' and resid 362 through 369 removed outlier: 3.710A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL A 378 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN A 459 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 3.771A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.208A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 579 through 581 removed outlier: 6.208A pdb=" N VAL H 91 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N HIS H 29 " --> pdb=" O LYS H 13 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 602 through 603 removed outlier: 3.610A pdb=" N MET A 637 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 789 through 790 Processing sheet with id=AB3, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AB4, first strand: chain 'A' and resid 902 through 905 Processing sheet with id=AB5, first strand: chain 'A' and resid 1140 through 1142 Processing sheet with id=AB6, first strand: chain 'A' and resid 1245 through 1247 removed outlier: 3.616A pdb=" N LEU A1257 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1214 " --> pdb=" O LEU A1257 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A1211 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE A1175 " --> pdb=" O LEU A1211 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG A1213 " --> pdb=" O THR A1173 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N THR A1173 " --> pdb=" O ARG A1213 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A1215 " --> pdb=" O ALA A1171 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N TYR A1177 " --> pdb=" O CYS I 52 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N CYS I 52 " --> pdb=" O TYR A1177 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1472 through 1475 Processing sheet with id=AB8, first strand: chain 'M' and resid 24 through 27 removed outlier: 5.942A pdb=" N LEU M 121 " --> pdb=" O MET M 61 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU M 63 " --> pdb=" O LEU M 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 242 through 243 removed outlier: 7.268A pdb=" N LEU M 341 " --> pdb=" O ILE M 364 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ILE M 364 " --> pdb=" O LEU M 341 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP M 343 " --> pdb=" O TYR M 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 272 through 275 removed outlier: 10.069A pdb=" N GLN M 272 " --> pdb=" O ASP M 454 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ILE M 456 " --> pdb=" O GLN M 272 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N ASP M 455 " --> pdb=" O PRO M 444 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 494 through 501 removed outlier: 7.285A pdb=" N VAL M 491 " --> pdb=" O PRO M 497 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY M 487 " --> pdb=" O ILE M 501 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE M 514 " --> pdb=" O GLN M 529 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLN M 529 " --> pdb=" O ILE M 514 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLU M 516 " --> pdb=" O MET M 527 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 87 through 93 removed outlier: 4.933A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP B 127 " --> pdb=" O GLN B 90 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY B 150 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 126 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 148 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE B 128 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LYS B 146 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LYS B 130 " --> pdb=" O HIS B 144 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N HIS B 144 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL B 132 " --> pdb=" O THR B 142 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N THR B 142 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AC5, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 394 Processing sheet with id=AC7, first strand: chain 'B' and resid 206 through 208 removed outlier: 3.557A pdb=" N TYR B 217 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE B 235 " --> pdb=" O CYS B 221 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC9, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AD1, first strand: chain 'B' and resid 551 through 552 removed outlier: 5.546A pdb=" N TRP B 573 " --> pdb=" O VAL B 569 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 569 " --> pdb=" O TRP B 573 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY B 575 " --> pdb=" O ILE B 567 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 748 through 751 removed outlier: 3.588A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE B 918 " --> pdb=" O VAL B 909 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL B 909 " --> pdb=" O PHE B 918 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS B 920 " --> pdb=" O VAL B 907 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 907 " --> pdb=" O LYS B 920 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG B 922 " --> pdb=" O ASP B 905 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR L 17 " --> pdb=" O ASN L 26 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD4, first strand: chain 'B' and resid 1025 through 1026 removed outlier: 7.152A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 827 through 829 Processing sheet with id=AD6, first strand: chain 'B' and resid 865 through 867 removed outlier: 6.790A pdb=" N THR B 894 " --> pdb=" O ILE B 866 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1113 through 1119 Processing sheet with id=AD8, first strand: chain 'B' and resid 1127 through 1129 Processing sheet with id=AD9, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.464A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU C 14 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 181 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 44 through 55 removed outlier: 5.165A pdb=" N ILE C 45 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY C 168 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE C 47 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS C 166 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG C 160 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ASN C 55 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU C 158 " --> pdb=" O ASN C 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.421A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 26 through 27 removed outlier: 4.516A pdb=" N ALA E 63 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N GLN E 71 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU E 103 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N PHE E 73 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL E 105 " --> pdb=" O PHE E 73 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE E 75 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 147 through 150 Processing sheet with id=AE5, first strand: chain 'F' and resid 56 through 57 Processing sheet with id=AE6, first strand: chain 'I' and resid 25 through 29 Processing sheet with id=AE7, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AE8, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE9, first strand: chain 'D' and resid 30 through 31 removed outlier: 6.056A pdb=" N LYS G 73 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ILE G 51 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ILE G 75 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N THR G 49 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE G 77 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N ALA G 47 " --> pdb=" O PHE G 77 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AF2, first strand: chain 'G' and resid 83 through 92 removed outlier: 6.612A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER G 105 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLY G 161 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N PHE G 107 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ASP G 156 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL G 152 " --> pdb=" O ASP G 156 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N PHE G 158 " --> pdb=" O THR G 150 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N THR G 150 " --> pdb=" O PHE G 158 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE G 160 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 147 " --> pdb=" O GLU G 83 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N GLU G 83 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 118 through 120 Processing sheet with id=AF4, first strand: chain 'Y' and resid 22 through 24 Processing sheet with id=AF5, first strand: chain 'Y' and resid 83 through 90 removed outlier: 7.116A pdb=" N GLY Y 59 " --> pdb=" O VAL Y 87 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL Y 89 " --> pdb=" O PHE Y 57 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE Y 57 " --> pdb=" O VAL Y 89 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER Z 214 " --> pdb=" O GLU Z 228 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 352 through 355 removed outlier: 3.996A pdb=" N PHE Z 358 " --> pdb=" O ASP Z 355 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TYR Z 366 " --> pdb=" O PHE Z 373 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N THR Z 302 " --> pdb=" O VAL Z 296 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N VAL Z 296 " --> pdb=" O THR Z 302 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER Z 304 " --> pdb=" O ASP Z 294 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 452 through 454 Processing sheet with id=AF8, first strand: chain 'Z' and resid 477 through 479 removed outlier: 5.843A pdb=" N ILE Z 492 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE Z 503 " --> pdb=" O ILE Z 492 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG Z 494 " --> pdb=" O ILE Z 501 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.494A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR Z 546 " --> pdb=" O LEU Z 542 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Z' and resid 586 through 587 Processing sheet with id=AG2, first strand: chain 'Z' and resid 635 through 639 removed outlier: 6.657A pdb=" N PHE Z 621 " --> pdb=" O LEU Z 617 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU Z 617 " --> pdb=" O PHE Z 621 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Z' and resid 742 through 746 removed outlier: 6.954A pdb=" N THR Z 731 " --> pdb=" O ALA Z 727 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA Z 727 " --> pdb=" O THR Z 731 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG Z 733 " --> pdb=" O LYS Z 725 " (cutoff:3.500A) 1547 hydrogen bonds defined for protein. 4293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 24.29 Time building geometry restraints manager: 17.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 8024 1.33 - 1.45: 10280 1.45 - 1.57: 23537 1.57 - 1.70: 179 1.70 - 1.82: 392 Bond restraints: 42412 Sorted by residual: bond pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 1.522 1.448 0.074 1.16e-02 7.43e+03 4.11e+01 bond pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 1.530 1.460 0.070 1.17e-02 7.31e+03 3.57e+01 bond pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " ideal model delta sigma weight residual 1.458 1.402 0.057 1.20e-02 6.94e+03 2.23e+01 bond pdb=" CA LYS Z 447 " pdb=" C LYS Z 447 " ideal model delta sigma weight residual 1.524 1.465 0.059 1.29e-02 6.01e+03 2.08e+01 bond pdb=" CA ILE Z 448 " pdb=" C ILE Z 448 " ideal model delta sigma weight residual 1.524 1.467 0.057 1.30e-02 5.92e+03 1.93e+01 ... (remaining 42407 not shown) Histogram of bond angle deviations from ideal: 94.16 - 102.25: 265 102.25 - 110.34: 10162 110.34 - 118.42: 23238 118.42 - 126.51: 23195 126.51 - 134.60: 788 Bond angle restraints: 57648 Sorted by residual: angle pdb=" N THR Z 449 " pdb=" CA THR Z 449 " pdb=" C THR Z 449 " ideal model delta sigma weight residual 111.28 94.45 16.83 1.35e+00 5.49e-01 1.55e+02 angle pdb=" C LYS M 449 " pdb=" N PRO M 450 " pdb=" CA PRO M 450 " ideal model delta sigma weight residual 120.21 131.08 -10.87 9.60e-01 1.09e+00 1.28e+02 angle pdb=" N ILE Z 450 " pdb=" CA ILE Z 450 " pdb=" C ILE Z 450 " ideal model delta sigma weight residual 109.21 94.16 15.05 1.36e+00 5.41e-01 1.22e+02 angle pdb=" N GLY Z 423 " pdb=" CA GLY Z 423 " pdb=" C GLY Z 423 " ideal model delta sigma weight residual 114.69 127.01 -12.32 1.19e+00 7.06e-01 1.07e+02 angle pdb=" N LYS Z 447 " pdb=" CA LYS Z 447 " pdb=" C LYS Z 447 " ideal model delta sigma weight residual 109.15 96.46 12.69 1.44e+00 4.82e-01 7.77e+01 ... (remaining 57643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.48: 25007 35.48 - 70.96: 717 70.96 - 106.44: 42 106.44 - 141.93: 2 141.93 - 177.41: 4 Dihedral angle restraints: 25772 sinusoidal: 11391 harmonic: 14381 Sorted by residual: dihedral pdb=" C5' G P 32 " pdb=" C4' G P 32 " pdb=" C3' G P 32 " pdb=" O3' G P 32 " ideal model delta sinusoidal sigma weight residual 82.00 152.92 -70.92 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" O4' G P 32 " pdb=" C4' G P 32 " pdb=" C3' G P 32 " pdb=" C2' G P 32 " ideal model delta sinusoidal sigma weight residual -35.00 31.43 -66.43 1 8.00e+00 1.56e-02 9.00e+01 dihedral pdb=" C3' G P 32 " pdb=" C4' G P 32 " pdb=" O4' G P 32 " pdb=" C1' G P 32 " ideal model delta sinusoidal sigma weight residual 20.00 -36.37 56.37 1 8.00e+00 1.56e-02 6.69e+01 ... (remaining 25769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 6316 0.134 - 0.268: 107 0.268 - 0.401: 6 0.401 - 0.535: 2 0.535 - 0.669: 4 Chirality restraints: 6435 Sorted by residual: chirality pdb=" C3' G P 36 " pdb=" C4' G P 36 " pdb=" O3' G P 36 " pdb=" C2' G P 36 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" CA TYR M 362 " pdb=" N TYR M 362 " pdb=" C TYR M 362 " pdb=" CB TYR M 362 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.48e+00 chirality pdb=" CA ASN M 324 " pdb=" N ASN M 324 " pdb=" C ASN M 324 " pdb=" CB ASN M 324 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.48e+00 ... (remaining 6432 not shown) Planarity restraints: 7144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR M 74 " 0.059 2.00e-02 2.50e+03 4.14e-02 3.42e+01 pdb=" CG TYR M 74 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR M 74 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR M 74 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR M 74 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR M 74 " -0.043 2.00e-02 2.50e+03 pdb=" CZ TYR M 74 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR M 74 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 35 " -0.059 2.00e-02 2.50e+03 4.03e-02 3.25e+01 pdb=" CG TYR M 35 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TYR M 35 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR M 35 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR M 35 " 0.032 2.00e-02 2.50e+03 pdb=" CE2 TYR M 35 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR M 35 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR M 35 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 120 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.77e+01 pdb=" N PRO G 121 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO G 121 " -0.068 5.00e-02 4.00e+02 pdb=" CD PRO G 121 " -0.070 5.00e-02 4.00e+02 ... (remaining 7141 not shown) Histogram of nonbonded interaction distances: 0.32 - 1.23: 62 1.23 - 2.15: 269 2.15 - 3.07: 27883 3.07 - 3.98: 113346 3.98 - 4.90: 207695 Warning: very small nonbonded interaction distances. Nonbonded interactions: 349255 Sorted by model distance: nonbonded pdb=" CZ ARG G 151 " pdb=" O ASP Z 505 " model vdw 0.317 3.270 nonbonded pdb=" O PRO M 461 " pdb=" N ASN M 465 " model vdw 0.346 2.520 nonbonded pdb=" CA MET Z 563 " pdb=" CE1 PHE Z 623 " model vdw 0.373 3.770 nonbonded pdb=" CG MET Z 563 " pdb=" CE2 PHE Z 623 " model vdw 0.384 3.740 nonbonded pdb=" CB PHE Z 499 " pdb=" CG ARG Z 555 " model vdw 0.430 3.840 ... (remaining 349250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.65 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 7.900 Check model and map are aligned: 0.580 Set scattering table: 0.350 Process input model: 126.350 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 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 : 0.005 0.079 42412 Z= 0.336 Angle : 0.844 16.828 57648 Z= 0.504 Chirality : 0.055 0.669 6435 Planarity : 0.006 0.134 7144 Dihedral : 15.209 177.407 16468 Min Nonbonded Distance : 0.317 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.10 % Favored : 94.84 % Rotamer: Outliers : 0.43 % Allowed : 1.17 % Favored : 98.40 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.21 (0.11), residues: 4882 helix: 0.00 (0.13), residues: 1526 sheet: -1.05 (0.18), residues: 710 loop : -1.19 (0.11), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP M 147 HIS 0.015 0.001 HIS M 94 PHE 0.061 0.003 PHE M 113 TYR 0.078 0.003 TYR M 74 ARG 0.016 0.001 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 616 time to evaluate : 4.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 900 SER cc_start: 0.9109 (m) cc_final: 0.8327 (p) REVERT: A 1086 MET cc_start: 0.8548 (mmm) cc_final: 0.8307 (mmm) REVERT: M 362 TYR cc_start: -0.3407 (OUTLIER) cc_final: -0.3667 (p90) REVERT: M 437 MET cc_start: 0.1135 (ptp) cc_final: -0.0167 (mmm) REVERT: B 368 MET cc_start: 0.8994 (mtp) cc_final: 0.8636 (ttt) REVERT: B 583 LEU cc_start: 0.8355 (tt) cc_final: 0.8140 (tp) REVERT: B 752 TYR cc_start: 0.7862 (m-10) cc_final: 0.6740 (m-10) REVERT: B 846 ASP cc_start: 0.7105 (p0) cc_final: 0.6880 (p0) REVERT: B 907 VAL cc_start: 0.7604 (t) cc_final: 0.6782 (t) REVERT: B 1159 PHE cc_start: 0.8945 (m-10) cc_final: 0.8696 (m-10) REVERT: C 243 THR cc_start: 0.8148 (t) cc_final: 0.7712 (t) REVERT: E 98 ASN cc_start: 0.7994 (p0) cc_final: 0.7775 (p0) REVERT: I 29 ASP cc_start: 0.8663 (t0) cc_final: 0.8446 (t70) REVERT: I 71 ASP cc_start: 0.7323 (p0) cc_final: 0.7046 (p0) REVERT: G 104 MET cc_start: 0.7836 (tmm) cc_final: 0.7103 (tmm) REVERT: Z 378 MET cc_start: -0.2919 (mtt) cc_final: -0.3638 (mtt) REVERT: Z 460 MET cc_start: 0.7292 (mmt) cc_final: 0.6999 (mmt) outliers start: 19 outliers final: 2 residues processed: 634 average time/residue: 0.5024 time to fit residues: 530.2430 Evaluate side-chains 372 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 369 time to evaluate : 5.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 362 TYR Chi-restraints excluded: chain M residue 425 LEU Chi-restraints excluded: chain M residue 463 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 418 optimal weight: 50.0000 chunk 375 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 200 optimal weight: 7.9990 chunk 388 optimal weight: 0.0030 chunk 150 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 289 optimal weight: 0.8980 chunk 450 optimal weight: 40.0000 overall best weight: 2.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 HIS A 441 GLN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** M 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 547 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN B 518 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 593 GLN B 683 GLN ** B 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 842 HIS B 980 HIS C 51 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** L 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 GLN Y 12 HIS Y 41 GLN Z 178 ASN ** Z 559 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 616 HIS ** Z 642 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 42412 Z= 0.283 Angle : 0.739 15.864 57648 Z= 0.387 Chirality : 0.048 0.289 6435 Planarity : 0.008 0.463 7144 Dihedral : 15.352 179.320 6467 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.61 % Rotamer: Outliers : 1.51 % Allowed : 9.13 % Favored : 89.35 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.12), residues: 4882 helix: 0.42 (0.13), residues: 1529 sheet: -0.75 (0.19), residues: 709 loop : -1.02 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP M 293 HIS 0.015 0.001 HIS Z 509 PHE 0.089 0.002 PHE Z 623 TYR 0.043 0.002 TYR Z 203 ARG 0.012 0.001 ARG M 564 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 368 time to evaluate : 4.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 520 MET cc_start: 0.8918 (mmm) cc_final: 0.8594 (mmp) REVERT: A 561 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8680 (mmm) REVERT: A 1228 MET cc_start: 0.8098 (mmm) cc_final: 0.7760 (mtt) REVERT: A 1459 MET cc_start: 0.7889 (mtt) cc_final: 0.7364 (mtt) REVERT: M 437 MET cc_start: 0.1619 (ptp) cc_final: 0.0398 (mmm) REVERT: B 53 MET cc_start: 0.8288 (mpp) cc_final: 0.8024 (mpp) REVERT: B 368 MET cc_start: 0.9008 (mtp) cc_final: 0.8802 (ttt) REVERT: B 394 ASP cc_start: 0.7544 (m-30) cc_final: 0.7172 (t70) REVERT: B 1172 MET cc_start: 0.7793 (mpp) cc_final: 0.7574 (mpp) REVERT: E 94 MET cc_start: 0.8235 (mmm) cc_final: 0.8009 (tpp) REVERT: K 38 GLU cc_start: 0.8130 (tp30) cc_final: 0.7652 (tp30) REVERT: K 50 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9341 (mt) REVERT: G 104 MET cc_start: 0.8040 (tmm) cc_final: 0.7538 (tmm) REVERT: G 158 PHE cc_start: 0.8312 (m-80) cc_final: 0.7989 (m-10) REVERT: Z 197 MET cc_start: 0.5605 (tpt) cc_final: 0.5335 (tpt) REVERT: Z 460 MET cc_start: 0.7350 (mmt) cc_final: 0.7095 (mmp) outliers start: 66 outliers final: 32 residues processed: 411 average time/residue: 0.4898 time to fit residues: 344.0486 Evaluate side-chains 345 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 311 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 561 MET Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 463 SER Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 111 ASN Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 758 LEU Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 508 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 250 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 374 optimal weight: 10.0000 chunk 306 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 451 optimal weight: 9.9990 chunk 487 optimal weight: 9.9990 chunk 401 optimal weight: 3.9990 chunk 447 optimal weight: 50.0000 chunk 153 optimal weight: 9.9990 chunk 361 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 HIS ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN A 884 ASN A1303 GLN M 90 GLN M 102 ASN M 243 GLN M 321 HIS B 52 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 518 HIS ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 725 GLN B1049 GLN B1060 HIS C 66 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 GLN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 60 GLN Z 737 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 42412 Z= 0.391 Angle : 0.753 20.095 57648 Z= 0.391 Chirality : 0.047 0.291 6435 Planarity : 0.006 0.249 7144 Dihedral : 15.045 175.563 6463 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.80 % Favored : 94.16 % Rotamer: Outliers : 2.75 % Allowed : 11.03 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.12), residues: 4882 helix: 0.54 (0.13), residues: 1539 sheet: -0.92 (0.19), residues: 722 loop : -0.89 (0.12), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 22 HIS 0.012 0.002 HIS Z 625 PHE 0.032 0.002 PHE Z 621 TYR 0.027 0.002 TYR B 766 ARG 0.013 0.001 ARG Z 619 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 298 time to evaluate : 5.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1228 MET cc_start: 0.8350 (mmm) cc_final: 0.8095 (mtt) REVERT: M 437 MET cc_start: 0.1829 (OUTLIER) cc_final: 0.0818 (mtt) REVERT: M 561 PHE cc_start: 0.4035 (OUTLIER) cc_final: 0.2700 (m-80) REVERT: B 485 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9097 (mt) REVERT: B 635 LEU cc_start: 0.8850 (tp) cc_final: 0.8640 (tt) REVERT: B 692 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9166 (p) REVERT: B 1172 MET cc_start: 0.8286 (mpp) cc_final: 0.7822 (mpp) REVERT: C 62 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 127 VAL cc_start: 0.9067 (t) cc_final: 0.8563 (p) REVERT: F 98 LYS cc_start: 0.9092 (mtmt) cc_final: 0.8846 (mtpp) REVERT: I 23 MET cc_start: 0.8401 (ttt) cc_final: 0.8129 (ttp) REVERT: K 50 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9477 (mm) REVERT: L 17 TYR cc_start: 0.7850 (m-80) cc_final: 0.7563 (m-80) REVERT: G 35 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7551 (mm-30) REVERT: G 101 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7730 (tp) REVERT: G 104 MET cc_start: 0.8419 (tmm) cc_final: 0.8099 (tmm) REVERT: Z 197 MET cc_start: 0.5902 (tpt) cc_final: 0.5688 (tpt) REVERT: Z 378 MET cc_start: -0.2798 (mtt) cc_final: -0.3870 (mmt) REVERT: Z 460 MET cc_start: 0.7489 (mmt) cc_final: 0.7019 (mmt) outliers start: 120 outliers final: 50 residues processed: 393 average time/residue: 0.4883 time to fit residues: 326.4730 Evaluate side-chains 294 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 238 time to evaluate : 4.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain M residue 561 PHE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 793 SER Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 2 ILE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 13 PHE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 26 ASN Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain Z residue 242 VAL Chi-restraints excluded: chain Z residue 493 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 445 optimal weight: 9.9990 chunk 339 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 215 optimal weight: 4.9990 chunk 302 optimal weight: 1.9990 chunk 452 optimal weight: 20.0000 chunk 479 optimal weight: 40.0000 chunk 236 optimal weight: 1.9990 chunk 429 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN A1299 GLN A1313 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 42412 Z= 0.225 Angle : 0.625 12.528 57648 Z= 0.324 Chirality : 0.044 0.249 6435 Planarity : 0.005 0.223 7144 Dihedral : 14.939 174.665 6462 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 2.08 % Allowed : 12.32 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.44 (0.12), residues: 4882 helix: 0.81 (0.14), residues: 1538 sheet: -0.80 (0.19), residues: 723 loop : -0.78 (0.12), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 49 HIS 0.009 0.001 HIS I 118 PHE 0.031 0.001 PHE Z 623 TYR 0.017 0.001 TYR F 56 ARG 0.008 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 270 time to evaluate : 5.176 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: A 329 MET cc_start: 0.8885 (tpp) cc_final: 0.8581 (tpp) REVERT: A 469 MET cc_start: 0.8130 (mtp) cc_final: 0.7905 (mtm) REVERT: A 501 MET cc_start: 0.7733 (mtt) cc_final: 0.7497 (mtp) REVERT: A 1228 MET cc_start: 0.8375 (mmm) cc_final: 0.8003 (mtt) REVERT: M 437 MET cc_start: 0.1702 (ptp) cc_final: 0.0844 (mtt) REVERT: B 485 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9019 (mt) REVERT: B 1054 MET cc_start: 0.8748 (mpp) cc_final: 0.8325 (mpp) REVERT: C 62 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7382 (tm-30) REVERT: F 98 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8854 (mtpp) REVERT: I 23 MET cc_start: 0.8398 (ttt) cc_final: 0.8124 (ttp) REVERT: K 38 GLU cc_start: 0.8183 (tp30) cc_final: 0.7983 (tp30) REVERT: K 50 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9427 (mt) REVERT: G 104 MET cc_start: 0.8384 (tmm) cc_final: 0.8136 (tmm) REVERT: Z 197 MET cc_start: 0.5878 (tpt) cc_final: 0.5670 (tpt) REVERT: Z 451 MET cc_start: 0.7767 (mmm) cc_final: 0.7315 (mmm) REVERT: Z 460 MET cc_start: 0.7371 (mmt) cc_final: 0.7155 (mmt) outliers start: 91 outliers final: 44 residues processed: 344 average time/residue: 0.5017 time to fit residues: 293.3988 Evaluate side-chains 289 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 4.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 757 GLN Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 149 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1149 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 103 ARG Chi-restraints excluded: chain K residue 14 GLU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain Z residue 493 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 399 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 356 optimal weight: 0.0070 chunk 197 optimal weight: 10.0000 chunk 409 optimal weight: 8.9990 chunk 331 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 244 optimal weight: 4.9990 chunk 430 optimal weight: 20.0000 chunk 120 optimal weight: 20.0000 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 121 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 42412 Z= 0.312 Angle : 0.639 12.695 57648 Z= 0.331 Chirality : 0.044 0.189 6435 Planarity : 0.004 0.153 7144 Dihedral : 14.840 175.131 6462 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.57 % Favored : 94.39 % Rotamer: Outliers : 2.50 % Allowed : 13.07 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.33 (0.12), residues: 4882 helix: 0.97 (0.14), residues: 1540 sheet: -0.80 (0.18), residues: 743 loop : -0.73 (0.12), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 22 HIS 0.005 0.001 HIS I 118 PHE 0.025 0.001 PHE Z 623 TYR 0.018 0.001 TYR F 56 ARG 0.005 0.000 ARG B 483 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 251 time to evaluate : 5.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 MET cc_start: 0.7819 (mtt) cc_final: 0.7608 (mtp) REVERT: A 769 MET cc_start: 0.8521 (tpp) cc_final: 0.8320 (mtt) REVERT: A 1228 MET cc_start: 0.8313 (mmm) cc_final: 0.8022 (mtt) REVERT: M 437 MET cc_start: 0.1894 (ptp) cc_final: 0.0921 (mtt) REVERT: B 218 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8841 (p) REVERT: B 840 MET cc_start: 0.7501 (tpp) cc_final: 0.7154 (tpp) REVERT: B 863 ASP cc_start: 0.6338 (t0) cc_final: 0.6024 (t0) REVERT: B 908 MET cc_start: 0.8420 (tmm) cc_final: 0.8078 (tmm) REVERT: B 1054 MET cc_start: 0.8724 (mpp) cc_final: 0.8272 (mpp) REVERT: E 95 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: F 98 LYS cc_start: 0.9152 (mtmt) cc_final: 0.8903 (mtpp) REVERT: I 23 MET cc_start: 0.8522 (ttt) cc_final: 0.8269 (ttp) REVERT: K 50 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9504 (mm) REVERT: G 104 MET cc_start: 0.8602 (tmm) cc_final: 0.8315 (tmm) REVERT: Z 197 MET cc_start: 0.6003 (tpt) cc_final: 0.5748 (tpt) REVERT: Z 378 MET cc_start: -0.3244 (mmm) cc_final: -0.4193 (mmt) REVERT: Z 451 MET cc_start: 0.8046 (mmm) cc_final: 0.7698 (mmm) REVERT: Z 460 MET cc_start: 0.7541 (mmt) cc_final: 0.7240 (mmt) outliers start: 109 outliers final: 60 residues processed: 337 average time/residue: 0.5376 time to fit residues: 315.1302 Evaluate side-chains 302 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 239 time to evaluate : 4.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 246 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 31 GLU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 24 LEU Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 150 THR Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain Z residue 493 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 161 optimal weight: 40.0000 chunk 431 optimal weight: 30.0000 chunk 94 optimal weight: 2.9990 chunk 281 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 479 optimal weight: 20.0000 chunk 398 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 251 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN A 441 GLN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN M 465 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.5928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 42412 Z= 0.362 Angle : 0.673 13.905 57648 Z= 0.346 Chirality : 0.045 0.225 6435 Planarity : 0.004 0.102 7144 Dihedral : 14.764 177.236 6462 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 2.63 % Allowed : 13.74 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 4882 helix: 0.97 (0.14), residues: 1554 sheet: -0.72 (0.19), residues: 726 loop : -0.76 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 506 HIS 0.012 0.001 HIS I 100 PHE 0.046 0.002 PHE G 107 TYR 0.019 0.002 TYR F 56 ARG 0.019 0.000 ARG Z 641 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 253 time to evaluate : 4.668 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: A 322 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8785 (mm) REVERT: A 769 MET cc_start: 0.8569 (tpp) cc_final: 0.8234 (mtt) REVERT: A 1228 MET cc_start: 0.8335 (mmm) cc_final: 0.8069 (mtt) REVERT: M 437 MET cc_start: 0.2267 (ptp) cc_final: 0.0625 (mmp) REVERT: B 218 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8933 (p) REVERT: B 485 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9033 (mt) REVERT: B 584 MET cc_start: 0.8139 (mmm) cc_final: 0.7936 (tpt) REVERT: B 692 THR cc_start: 0.9652 (OUTLIER) cc_final: 0.9309 (p) REVERT: B 744 MET cc_start: 0.8794 (mmm) cc_final: 0.8520 (mmm) REVERT: B 791 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7977 (tp30) REVERT: B 840 MET cc_start: 0.8215 (tpp) cc_final: 0.7769 (tpp) REVERT: B 863 ASP cc_start: 0.6751 (t0) cc_final: 0.6423 (t0) REVERT: B 908 MET cc_start: 0.8597 (tmm) cc_final: 0.8322 (tmm) REVERT: B 1054 MET cc_start: 0.8683 (mpp) cc_final: 0.8177 (mpp) REVERT: E 18 MET cc_start: 0.8897 (mmm) cc_final: 0.8609 (mmm) REVERT: E 94 MET cc_start: 0.8730 (mmm) cc_final: 0.8372 (mmm) REVERT: F 57 MET cc_start: 0.8816 (tmm) cc_final: 0.8601 (tmm) REVERT: F 98 LYS cc_start: 0.9154 (mtmt) cc_final: 0.8922 (mtpp) REVERT: H 37 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6907 (ttp) REVERT: I 23 MET cc_start: 0.8621 (ttt) cc_final: 0.8411 (ttp) REVERT: K 50 LEU cc_start: 0.9776 (OUTLIER) cc_final: 0.9567 (mm) REVERT: G 104 MET cc_start: 0.8624 (tmm) cc_final: 0.8234 (tmm) REVERT: Z 197 MET cc_start: 0.5817 (tpt) cc_final: 0.5546 (tpt) REVERT: Z 378 MET cc_start: -0.3096 (mmm) cc_final: -0.4025 (mmt) REVERT: Z 451 MET cc_start: 0.8057 (mmm) cc_final: 0.7784 (mmm) REVERT: Z 460 MET cc_start: 0.7697 (mmt) cc_final: 0.7376 (mmt) outliers start: 115 outliers final: 64 residues processed: 344 average time/residue: 0.4779 time to fit residues: 283.9349 Evaluate side-chains 305 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 234 time to evaluate : 4.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 246 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 763 SER Chi-restraints excluded: chain B residue 791 GLU Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain J residue 36 ASP Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 462 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 273 optimal weight: 1.9990 chunk 350 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 403 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 478 optimal weight: 8.9990 chunk 299 optimal weight: 0.9990 chunk 291 optimal weight: 0.9980 chunk 220 optimal weight: 7.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** B1094 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 HIS ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 42412 Z= 0.177 Angle : 0.611 13.353 57648 Z= 0.313 Chirality : 0.043 0.210 6435 Planarity : 0.004 0.074 7144 Dihedral : 14.612 175.968 6462 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.24 % Favored : 94.72 % Rotamer: Outliers : 2.01 % Allowed : 14.81 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.19 (0.12), residues: 4882 helix: 1.14 (0.14), residues: 1544 sheet: -0.79 (0.18), residues: 769 loop : -0.66 (0.13), residues: 2569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 49 HIS 0.005 0.001 HIS A 465 PHE 0.022 0.001 PHE G 107 TYR 0.015 0.001 TYR A 827 ARG 0.008 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 262 time to evaluate : 4.779 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: A 196 LEU cc_start: 0.9092 (mt) cc_final: 0.8874 (mt) REVERT: M 418 ILE cc_start: -0.0416 (OUTLIER) cc_final: -0.0689 (mm) REVERT: M 437 MET cc_start: 0.2369 (OUTLIER) cc_final: 0.0644 (mmp) REVERT: M 485 ASN cc_start: 0.7517 (m-40) cc_final: 0.7306 (m-40) REVERT: B 485 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.9021 (mt) REVERT: B 692 THR cc_start: 0.9562 (OUTLIER) cc_final: 0.9265 (p) REVERT: B 744 MET cc_start: 0.8695 (mmm) cc_final: 0.8421 (tpt) REVERT: B 791 GLU cc_start: 0.8339 (tp30) cc_final: 0.7919 (tp30) REVERT: B 840 MET cc_start: 0.8239 (tpp) cc_final: 0.7964 (mmt) REVERT: B 863 ASP cc_start: 0.6704 (t0) cc_final: 0.6295 (t0) REVERT: B 908 MET cc_start: 0.8506 (tmm) cc_final: 0.8236 (tmm) REVERT: E 18 MET cc_start: 0.8797 (mmm) cc_final: 0.8585 (mmm) REVERT: E 94 MET cc_start: 0.8599 (mmm) cc_final: 0.8269 (mmm) REVERT: F 98 LYS cc_start: 0.9160 (mtmt) cc_final: 0.8909 (mtpp) REVERT: K 50 LEU cc_start: 0.9692 (OUTLIER) cc_final: 0.9482 (mt) REVERT: K 80 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7871 (p0) REVERT: L 25 GLU cc_start: 0.8803 (mp0) cc_final: 0.8570 (mp0) REVERT: L 37 ARG cc_start: 0.8045 (ptt-90) cc_final: 0.7774 (ptt-90) REVERT: G 104 MET cc_start: 0.8479 (tmm) cc_final: 0.8251 (tmm) REVERT: Z 197 MET cc_start: 0.5697 (tpt) cc_final: 0.5446 (tpt) REVERT: Z 451 MET cc_start: 0.8191 (mmm) cc_final: 0.7930 (mmm) REVERT: Z 460 MET cc_start: 0.7644 (mmt) cc_final: 0.7317 (mmt) REVERT: Z 508 MET cc_start: 0.6021 (tpt) cc_final: 0.5572 (mmt) outliers start: 88 outliers final: 52 residues processed: 331 average time/residue: 0.4949 time to fit residues: 280.1036 Evaluate side-chains 299 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 241 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 418 ILE Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 295 optimal weight: 3.9990 chunk 190 optimal weight: 20.0000 chunk 285 optimal weight: 0.0770 chunk 144 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 303 optimal weight: 8.9990 chunk 325 optimal weight: 7.9990 chunk 236 optimal weight: 0.5980 chunk 44 optimal weight: 4.9990 chunk 375 optimal weight: 6.9990 overall best weight: 3.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS Y 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 42412 Z= 0.265 Angle : 0.632 13.178 57648 Z= 0.322 Chirality : 0.043 0.335 6435 Planarity : 0.004 0.074 7144 Dihedral : 14.544 176.767 6462 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 1.81 % Allowed : 15.25 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 4882 helix: 1.19 (0.14), residues: 1546 sheet: -0.70 (0.18), residues: 763 loop : -0.65 (0.13), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.005 0.001 HIS B 939 PHE 0.026 0.001 PHE A 458 TYR 0.023 0.001 TYR B1048 ARG 0.009 0.000 ARG B1050 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 241 time to evaluate : 4.824 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 196 LEU cc_start: 0.9110 (mt) cc_final: 0.8875 (mt) REVERT: M 418 ILE cc_start: -0.0492 (OUTLIER) cc_final: -0.0742 (mm) REVERT: M 437 MET cc_start: 0.2513 (OUTLIER) cc_final: 0.0728 (mmp) REVERT: B 485 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8983 (mt) REVERT: B 692 THR cc_start: 0.9616 (OUTLIER) cc_final: 0.9315 (p) REVERT: B 744 MET cc_start: 0.8722 (mmm) cc_final: 0.8462 (mmm) REVERT: B 791 GLU cc_start: 0.8391 (tp30) cc_final: 0.7932 (tp30) REVERT: B 840 MET cc_start: 0.8511 (tpp) cc_final: 0.8237 (mmt) REVERT: B 863 ASP cc_start: 0.6899 (t0) cc_final: 0.6510 (t0) REVERT: B 908 MET cc_start: 0.8571 (tmm) cc_final: 0.8291 (tmm) REVERT: E 18 MET cc_start: 0.8782 (mmm) cc_final: 0.8534 (mmm) REVERT: E 94 MET cc_start: 0.8706 (mmm) cc_final: 0.8353 (mmm) REVERT: F 98 LYS cc_start: 0.9170 (mtmt) cc_final: 0.8927 (mtpp) REVERT: K 38 GLU cc_start: 0.8008 (tp30) cc_final: 0.7600 (tp30) REVERT: G 104 MET cc_start: 0.8456 (tmm) cc_final: 0.8248 (tmm) REVERT: Z 197 MET cc_start: 0.5698 (tpt) cc_final: 0.5451 (tpt) REVERT: Z 378 MET cc_start: -0.3455 (mmt) cc_final: -0.3661 (mmt) REVERT: Z 451 MET cc_start: 0.8211 (mmm) cc_final: 0.7936 (mmm) REVERT: Z 460 MET cc_start: 0.7668 (mmt) cc_final: 0.7319 (mmt) outliers start: 79 outliers final: 60 residues processed: 301 average time/residue: 0.4969 time to fit residues: 259.1954 Evaluate side-chains 298 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 234 time to evaluate : 4.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 418 ILE Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 434 optimal weight: 9.9990 chunk 457 optimal weight: 7.9990 chunk 417 optimal weight: 5.9990 chunk 445 optimal weight: 50.0000 chunk 268 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 349 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 402 optimal weight: 0.8980 chunk 421 optimal weight: 5.9990 chunk 443 optimal weight: 5.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 42412 Z= 0.242 Angle : 0.633 14.255 57648 Z= 0.322 Chirality : 0.044 0.446 6435 Planarity : 0.004 0.064 7144 Dihedral : 14.503 176.878 6462 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.57 % Favored : 94.39 % Rotamer: Outliers : 1.76 % Allowed : 15.59 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.20 (0.12), residues: 4882 helix: 1.07 (0.14), residues: 1565 sheet: -0.71 (0.18), residues: 768 loop : -0.66 (0.13), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 49 HIS 0.006 0.001 HIS G 111 PHE 0.022 0.001 PHE A 458 TYR 0.015 0.001 TYR A 827 ARG 0.005 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 246 time to evaluate : 5.134 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 196 LEU cc_start: 0.9103 (mt) cc_final: 0.8872 (mt) REVERT: M 61 MET cc_start: 0.1942 (tpp) cc_final: 0.0951 (tpp) REVERT: M 437 MET cc_start: 0.2657 (OUTLIER) cc_final: 0.0764 (mmp) REVERT: M 485 ASN cc_start: 0.6994 (m-40) cc_final: 0.6603 (m-40) REVERT: B 485 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8988 (mt) REVERT: B 692 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9282 (p) REVERT: B 744 MET cc_start: 0.8705 (mmm) cc_final: 0.8433 (mmm) REVERT: B 791 GLU cc_start: 0.8389 (tp30) cc_final: 0.7919 (tp30) REVERT: B 840 MET cc_start: 0.8452 (tpp) cc_final: 0.8148 (mmt) REVERT: B 863 ASP cc_start: 0.6959 (t0) cc_final: 0.6522 (t0) REVERT: B 908 MET cc_start: 0.8554 (tmm) cc_final: 0.8241 (tmm) REVERT: E 18 MET cc_start: 0.8775 (mmm) cc_final: 0.8498 (mmm) REVERT: E 94 MET cc_start: 0.8611 (mmm) cc_final: 0.8229 (mmm) REVERT: F 98 LYS cc_start: 0.9170 (mtmt) cc_final: 0.8933 (mtpp) REVERT: K 38 GLU cc_start: 0.7926 (tp30) cc_final: 0.7495 (tp30) REVERT: K 80 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7918 (p0) REVERT: G 35 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7730 (mm-30) REVERT: Z 197 MET cc_start: 0.5687 (tpt) cc_final: 0.5428 (tpt) REVERT: Z 378 MET cc_start: -0.3248 (mmt) cc_final: -0.3467 (mmt) REVERT: Z 451 MET cc_start: 0.8229 (mmm) cc_final: 0.7984 (mmm) REVERT: Z 460 MET cc_start: 0.7672 (mmt) cc_final: 0.7356 (mmt) outliers start: 77 outliers final: 64 residues processed: 304 average time/residue: 0.5032 time to fit residues: 263.3858 Evaluate side-chains 305 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 237 time to evaluate : 5.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 539 GLN Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 861 GLN Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1166 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain B residue 1049 GLN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain I residue 100 HIS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain K residue 45 ILE Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 292 optimal weight: 9.9990 chunk 471 optimal weight: 8.9990 chunk 287 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 327 optimal weight: 0.4980 chunk 494 optimal weight: 20.0000 chunk 454 optimal weight: 0.0980 chunk 393 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 303 optimal weight: 3.9990 chunk 241 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 502 ASN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 HIS ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 89 ASN ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 42412 Z= 0.180 Angle : 0.638 16.276 57648 Z= 0.322 Chirality : 0.044 0.346 6435 Planarity : 0.004 0.061 7144 Dihedral : 14.461 176.543 6462 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer: Outliers : 1.53 % Allowed : 15.80 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.18 (0.12), residues: 4882 helix: 1.09 (0.14), residues: 1562 sheet: -0.69 (0.18), residues: 760 loop : -0.66 (0.13), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 236 HIS 0.028 0.001 HIS I 118 PHE 0.021 0.001 PHE A 458 TYR 0.017 0.001 TYR B 388 ARG 0.005 0.000 ARG G 16 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9764 Ramachandran restraints generated. 4882 Oldfield, 0 Emsley, 4882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 248 time to evaluate : 4.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.9057 (mt) cc_final: 0.8849 (mt) REVERT: M 61 MET cc_start: 0.2018 (tpp) cc_final: 0.0996 (tpp) REVERT: M 276 MET cc_start: 0.1023 (tmm) cc_final: 0.0528 (tmm) REVERT: M 437 MET cc_start: 0.2467 (OUTLIER) cc_final: 0.0667 (mmp) REVERT: M 485 ASN cc_start: 0.7136 (m-40) cc_final: 0.6911 (m-40) REVERT: B 485 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8992 (mt) REVERT: B 692 THR cc_start: 0.9574 (OUTLIER) cc_final: 0.9274 (p) REVERT: B 744 MET cc_start: 0.8674 (mmm) cc_final: 0.8390 (tpt) REVERT: B 791 GLU cc_start: 0.8376 (tp30) cc_final: 0.7223 (tp30) REVERT: B 840 MET cc_start: 0.8382 (tpp) cc_final: 0.8110 (mmt) REVERT: B 863 ASP cc_start: 0.6990 (t0) cc_final: 0.6564 (t0) REVERT: B 908 MET cc_start: 0.8537 (tmm) cc_final: 0.8247 (tmm) REVERT: E 94 MET cc_start: 0.8570 (mmm) cc_final: 0.8194 (mmm) REVERT: F 98 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8931 (mtpp) REVERT: K 38 GLU cc_start: 0.7909 (tp30) cc_final: 0.7553 (tp30) REVERT: Y 48 MET cc_start: 0.1264 (tmm) cc_final: 0.0982 (ptt) REVERT: Z 197 MET cc_start: 0.5571 (tpt) cc_final: 0.5294 (tpt) REVERT: Z 451 MET cc_start: 0.8219 (mmm) cc_final: 0.7984 (mmm) REVERT: Z 460 MET cc_start: 0.7650 (mmt) cc_final: 0.7345 (mmp) REVERT: Z 563 MET cc_start: -0.1242 (tpp) cc_final: -0.1660 (mmm) outliers start: 67 outliers final: 56 residues processed: 301 average time/residue: 0.4924 time to fit residues: 258.1855 Evaluate side-chains 299 residues out of total 4388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 240 time to evaluate : 4.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 439 HIS Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 502 ASN Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 872 MET Chi-restraints excluded: chain A residue 1021 VAL Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1436 VAL Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 237 THR Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 398 THR Chi-restraints excluded: chain M residue 437 MET Chi-restraints excluded: chain M residue 535 PHE Chi-restraints excluded: chain M residue 558 LEU Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 668 LEU Chi-restraints excluded: chain B residue 681 ASP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1041 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain E residue 65 ASN Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain E residue 199 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 133 HIS Chi-restraints excluded: chain J residue 13 ILE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain D residue 24 LYS Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain G residue 93 ASN Chi-restraints excluded: chain G residue 101 ILE Chi-restraints excluded: chain G residue 150 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 496 random chunks: chunk 312 optimal weight: 5.9990 chunk 419 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 362 optimal weight: 0.0000 chunk 58 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 394 optimal weight: 0.9980 chunk 164 optimal weight: 20.0000 chunk 404 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 23 HIS ** D 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.074939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.045192 restraints weight = 209197.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.045110 restraints weight = 103686.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.045812 restraints weight = 67867.869| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.6532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 42412 Z= 0.197 Angle : 0.637 14.633 57648 Z= 0.323 Chirality : 0.043 0.335 6435 Planarity : 0.004 0.056 7144 Dihedral : 14.403 176.860 6462 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 1.56 % Allowed : 15.77 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.16 (0.12), residues: 4882 helix: 1.09 (0.14), residues: 1562 sheet: -0.66 (0.18), residues: 774 loop : -0.64 (0.13), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 49 HIS 0.026 0.001 HIS I 118 PHE 0.021 0.001 PHE K 13 TYR 0.016 0.001 TYR B 388 ARG 0.006 0.000 ARG G 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8281.08 seconds wall clock time: 151 minutes 51.96 seconds (9111.96 seconds total)