Starting phenix.real_space_refine on Tue Jul 7 01:34:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyv_18764/07_2026/8qyv_18764.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyv_18764/07_2026/8qyv_18764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyv_18764/07_2026/8qyv_18764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyv_18764/07_2026/8qyv_18764.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyv_18764/07_2026/8qyv_18764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyv_18764/07_2026/8qyv_18764.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 252 5.49 5 Mg 8 5.21 5 S 121 5.16 5 Be 2 3.05 5 C 25680 2.51 5 N 7416 2.21 5 O 8511 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 41998 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 728 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 755 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 683 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 521 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 69} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "E" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 715 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "G" Number of atoms: 640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 640 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 2402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2402 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "J" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2436 Classifications: {'DNA': 118} Link IDs: {'rna3p': 117} Chain: "M" Number of atoms: 5562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5562 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 20, 'TRANS': 699} Unresolved non-hydrogen bonds: 343 Unresolved non-hydrogen angles: 431 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ARG:plan': 7, 'TYR:plan': 4, 'HIS:plan': 1, 'ASN:plan1': 5, 'GLU:plan': 10, 'GLN:plan1': 8, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 6} Unresolved non-hydrogen planarities: 236 Chain: "P" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 872 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1675 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 196} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 3313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3313 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 18, 'TRANS': 420} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'TYR:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "U" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3424 Classifications: {'peptide': 446} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 435} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "V" Number of atoms: 3245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3245 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 408} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 26 Chain: "W" Number of atoms: 3303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3303 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 25 Chain: "X" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3371 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "Y" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3342 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 10, 'TRANS': 432} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'GLN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "Z" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1442 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 86 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'TYR:plan': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20084 SG CYS S 244 67.626 84.811 57.910 1.00250.07 S ATOM 20104 SG CYS S 247 68.324 88.135 55.433 1.00260.28 S ATOM 20245 SG CYS S 268 67.383 89.041 57.104 1.00258.39 S ATOM 20164 SG CYS S 256 65.626 84.210 68.272 1.00245.31 S ATOM 20185 SG CYS S 259 63.723 81.835 66.014 1.00258.70 S ATOM 20324 SG CYS S 277 61.793 84.258 68.261 1.00279.70 S Time building chain proxies: 9.81, per 1000 atoms: 0.23 Number of scatterers: 41998 At special positions: 0 Unit cell: (199.75, 190.4, 179.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 121 16.00 P 252 15.00 Mg 8 11.99 F 6 9.00 O 8511 8.00 N 7416 7.00 C 25680 6.00 Be 2 4.00 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " Number of angles added : 3 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8984 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 38 sheets defined 50.3% alpha, 9.3% beta 111 base pairs and 189 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.163A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 114 removed outlier: 3.704A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.845A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.587A pdb=" N LEU B 48 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 76 Processing helix chain 'B' and resid 85 through 114 removed outlier: 4.040A pdb=" N ALA B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.716A pdb=" N ILE B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 41 Processing helix chain 'C' and resid 49 through 76 removed outlier: 4.093A pdb=" N GLU C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N GLU C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N SER C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 removed outlier: 4.031A pdb=" N VAL C 86 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 87 " --> pdb=" O SER C 83 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR C 88 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 removed outlier: 3.700A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 removed outlier: 3.510A pdb=" N GLY D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 75 removed outlier: 4.172A pdb=" N GLU D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N SER D 69 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 27 through 39 removed outlier: 3.718A pdb=" N VAL E 31 " --> pdb=" O PRO E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 74 removed outlier: 3.507A pdb=" N LEU E 56 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN E 74 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 91 removed outlier: 4.002A pdb=" N ASP E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 98 Processing helix chain 'G' and resid 40 through 52 removed outlier: 3.577A pdb=" N ILE G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 87 removed outlier: 3.694A pdb=" N ASN G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 105 removed outlier: 4.091A pdb=" N LEU G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 126 removed outlier: 3.969A pdb=" N HIS G 112 " --> pdb=" O GLU G 108 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER G 126 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing helix chain 'M' and resid 699 through 713 removed outlier: 4.114A pdb=" N GLY M 703 " --> pdb=" O TYR M 699 " (cutoff:3.500A) Processing helix chain 'M' and resid 726 through 742 Processing helix chain 'M' and resid 756 through 767 removed outlier: 3.841A pdb=" N GLU M 761 " --> pdb=" O LEU M 757 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE M 764 " --> pdb=" O TRP M 760 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS M 765 " --> pdb=" O GLU M 761 " (cutoff:3.500A) Processing helix chain 'M' and resid 779 through 787 Processing helix chain 'M' and resid 803 through 807 removed outlier: 4.194A pdb=" N VAL M 807 " --> pdb=" O TYR M 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 803 through 807' Processing helix chain 'M' and resid 809 through 814 Processing helix chain 'M' and resid 826 through 829 Processing helix chain 'M' and resid 834 through 842 removed outlier: 3.718A pdb=" N GLN M 838 " --> pdb=" O SER M 834 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU M 840 " --> pdb=" O ARG M 836 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN M 842 " --> pdb=" O GLN M 838 " (cutoff:3.500A) Processing helix chain 'M' and resid 860 through 871 Processing helix chain 'M' and resid 888 through 893 removed outlier: 4.090A pdb=" N GLN M 892 " --> pdb=" O ASP M 888 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TRP M 893 " --> pdb=" O ALA M 889 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 888 through 893' Processing helix chain 'M' and resid 895 through 904 Processing helix chain 'M' and resid 907 through 911 Processing helix chain 'M' and resid 913 through 926 removed outlier: 3.537A pdb=" N THR M 917 " --> pdb=" O GLU M 913 " (cutoff:3.500A) Processing helix chain 'M' and resid 927 through 929 No H-bonds generated for 'chain 'M' and resid 927 through 929' Processing helix chain 'M' and resid 954 through 973 removed outlier: 3.642A pdb=" N THR M 973 " --> pdb=" O GLN M 969 " (cutoff:3.500A) Processing helix chain 'M' and resid 981 through 994 removed outlier: 4.418A pdb=" N CYS M 985 " --> pdb=" O SER M 981 " (cutoff:3.500A) Processing helix chain 'M' and resid 1014 through 1030 removed outlier: 3.654A pdb=" N TYR M1018 " --> pdb=" O VAL M1014 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP M1020 " --> pdb=" O SER M1016 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL M1021 " --> pdb=" O ASP M1017 " (cutoff:3.500A) Processing helix chain 'M' and resid 1046 through 1050 removed outlier: 3.685A pdb=" N LEU M1049 " --> pdb=" O VAL M1046 " (cutoff:3.500A) Processing helix chain 'M' and resid 1055 through 1065 Processing helix chain 'M' and resid 1070 through 1089 removed outlier: 3.685A pdb=" N GLU M1074 " --> pdb=" O ASN M1070 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) Processing helix chain 'M' and resid 1095 through 1101 Processing helix chain 'M' and resid 1104 through 1133 Processing helix chain 'M' and resid 1140 through 1148 Processing helix chain 'M' and resid 1165 through 1173 removed outlier: 3.913A pdb=" N LEU M1171 " --> pdb=" O GLN M1167 " (cutoff:3.500A) Processing helix chain 'M' and resid 1173 through 1180 Processing helix chain 'M' and resid 1192 through 1197 removed outlier: 3.952A pdb=" N LEU M1197 " --> pdb=" O ARG M1193 " (cutoff:3.500A) Processing helix chain 'M' and resid 1208 through 1220 removed outlier: 3.517A pdb=" N VAL M1213 " --> pdb=" O THR M1209 " (cutoff:3.500A) Processing helix chain 'M' and resid 1224 through 1231 Processing helix chain 'M' and resid 1239 through 1244 Processing helix chain 'M' and resid 1245 through 1261 removed outlier: 3.732A pdb=" N GLN M1249 " --> pdb=" O CYS M1245 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS M1250 " --> pdb=" O GLY M1246 " (cutoff:3.500A) Processing helix chain 'M' and resid 1271 through 1285 removed outlier: 3.806A pdb=" N LEU M1275 " --> pdb=" O MET M1271 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP M1276 " --> pdb=" O THR M1272 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL M1277 " --> pdb=" O LYS M1273 " (cutoff:3.500A) Processing helix chain 'M' and resid 1297 through 1310 Processing helix chain 'M' and resid 1344 through 1353 removed outlier: 4.132A pdb=" N ASP M1348 " --> pdb=" O ASN M1344 " (cutoff:3.500A) Processing helix chain 'M' and resid 1374 through 1392 removed outlier: 4.250A pdb=" N ASN M1378 " --> pdb=" O THR M1374 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN M1391 " --> pdb=" O ARG M1387 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 204 Processing helix chain 'P' and resid 222 through 227 Processing helix chain 'P' and resid 237 through 253 Processing helix chain 'P' and resid 254 through 265 Processing helix chain 'P' and resid 266 through 303 removed outlier: 3.647A pdb=" N GLN P 270 " --> pdb=" O PHE P 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 46 Processing helix chain 'R' and resid 68 through 79 removed outlier: 4.522A pdb=" N GLU R 72 " --> pdb=" O LEU R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 121 Processing helix chain 'R' and resid 132 through 137 removed outlier: 4.249A pdb=" N PHE R 136 " --> pdb=" O PRO R 132 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 132 through 137' Processing helix chain 'R' and resid 138 through 142 Processing helix chain 'R' and resid 219 through 235 Processing helix chain 'R' and resid 241 through 252 removed outlier: 3.876A pdb=" N VAL R 245 " --> pdb=" O GLU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 266 Processing helix chain 'R' and resid 308 through 313 removed outlier: 3.615A pdb=" N ILE R 313 " --> pdb=" O GLU R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 318 removed outlier: 3.514A pdb=" N PHE R 317 " --> pdb=" O PRO R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 324 Processing helix chain 'R' and resid 329 through 341 Processing helix chain 'R' and resid 345 through 351 removed outlier: 3.650A pdb=" N MET R 349 " --> pdb=" O VAL R 345 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL R 350 " --> pdb=" O ARG R 346 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY R 351 " --> pdb=" O PRO R 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 345 through 351' Processing helix chain 'R' and resid 358 through 362 removed outlier: 3.622A pdb=" N ASN R 361 " --> pdb=" O GLY R 358 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 377 Processing helix chain 'R' and resid 391 through 406 removed outlier: 3.909A pdb=" N PHE R 395 " --> pdb=" O ASP R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 413 removed outlier: 3.618A pdb=" N LYS R 411 " --> pdb=" O ASP R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 415 through 422 removed outlier: 3.622A pdb=" N TYR R 419 " --> pdb=" O THR R 415 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS R 422 " --> pdb=" O GLU R 418 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 430 removed outlier: 3.778A pdb=" N CYS R 427 " --> pdb=" O GLY R 423 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 90 removed outlier: 3.567A pdb=" N ARG S 89 " --> pdb=" O SER S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 107 removed outlier: 3.567A pdb=" N THR S 107 " --> pdb=" O MET S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 125 Processing helix chain 'S' and resid 127 through 135 removed outlier: 3.554A pdb=" N THR S 135 " --> pdb=" O ILE S 131 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 179 removed outlier: 4.510A pdb=" N GLN S 176 " --> pdb=" O LEU S 172 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU S 177 " --> pdb=" O ARG S 173 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER S 178 " --> pdb=" O GLU S 174 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR S 179 " --> pdb=" O ILE S 175 " (cutoff:3.500A) Processing helix chain 'S' and resid 192 through 203 Processing helix chain 'S' and resid 207 through 214 Processing helix chain 'S' and resid 218 through 227 Processing helix chain 'S' and resid 265 through 275 removed outlier: 4.165A pdb=" N GLU S 274 " --> pdb=" O LYS S 270 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR S 275 " --> pdb=" O LEU S 271 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.643A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 108 through 111 removed outlier: 3.587A pdb=" N TYR T 111 " --> pdb=" O SER T 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 108 through 111' Processing helix chain 'T' and resid 116 through 127 Processing helix chain 'T' and resid 182 through 193 Processing helix chain 'T' and resid 216 through 219 Processing helix chain 'T' and resid 249 through 258 Processing helix chain 'T' and resid 264 through 273 removed outlier: 3.550A pdb=" N MET T 268 " --> pdb=" O ASP T 264 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.731A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 Processing helix chain 'T' and resid 317 through 329 removed outlier: 3.635A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 360 through 367 Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 429 removed outlier: 3.940A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 457 removed outlier: 3.856A pdb=" N GLU T 457 " --> pdb=" O THR T 453 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 81 through 93 Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'U' and resid 112 through 124 removed outlier: 3.575A pdb=" N SER U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 182 removed outlier: 3.594A pdb=" N GLY U 178 " --> pdb=" O LYS U 174 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU U 182 " --> pdb=" O GLY U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 209 through 213 Processing helix chain 'U' and resid 241 through 250 removed outlier: 3.924A pdb=" N ARG U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 255 through 260 Processing helix chain 'U' and resid 266 through 283 removed outlier: 3.713A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 301 Processing helix chain 'U' and resid 302 through 313 removed outlier: 3.685A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 343 Processing helix chain 'U' and resid 344 through 351 Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.785A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 432 through 443 Processing helix chain 'V' and resid 51 through 68 removed outlier: 3.850A pdb=" N LYS V 68 " --> pdb=" O LEU V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 97 Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.545A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 129 removed outlier: 4.055A pdb=" N ILE V 129 " --> pdb=" O PHE V 125 " (cutoff:3.500A) Processing helix chain 'V' and resid 182 through 192 Processing helix chain 'V' and resid 217 through 219 No H-bonds generated for 'chain 'V' and resid 217 through 219' Processing helix chain 'V' and resid 249 through 258 removed outlier: 4.020A pdb=" N ASN V 256 " --> pdb=" O LEU V 252 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 274 removed outlier: 4.071A pdb=" N LYS V 274 " --> pdb=" O GLY V 270 " (cutoff:3.500A) Processing helix chain 'V' and resid 281 through 298 removed outlier: 3.580A pdb=" N ARG V 285 " --> pdb=" O THR V 281 " (cutoff:3.500A) Processing helix chain 'V' and resid 313 through 316 Processing helix chain 'V' and resid 317 through 329 removed outlier: 4.002A pdb=" N GLU V 329 " --> pdb=" O ASN V 325 " (cutoff:3.500A) Processing helix chain 'V' and resid 360 through 366 removed outlier: 3.788A pdb=" N ARG V 366 " --> pdb=" O ASP V 362 " (cutoff:3.500A) Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 418 removed outlier: 3.626A pdb=" N ALA V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 429 Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 458 Processing helix chain 'W' and resid 47 through 64 removed outlier: 3.570A pdb=" N GLY W 64 " --> pdb=" O MET W 60 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 93 Processing helix chain 'W' and resid 104 through 106 No H-bonds generated for 'chain 'W' and resid 104 through 106' Processing helix chain 'W' and resid 112 through 123 Processing helix chain 'W' and resid 173 through 182 removed outlier: 3.775A pdb=" N ASP W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU W 182 " --> pdb=" O GLY W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 250 removed outlier: 4.289A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 251 through 254 removed outlier: 4.262A pdb=" N PHE W 254 " --> pdb=" O THR W 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 251 through 254' Processing helix chain 'W' and resid 255 through 260 Processing helix chain 'W' and resid 266 through 284 removed outlier: 3.835A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR W 275 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 302 through 313 Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.803A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 3.903A pdb=" N SER W 399 " --> pdb=" O SER W 395 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 Processing helix chain 'W' and resid 432 through 443 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.587A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 removed outlier: 3.800A pdb=" N ALA X 89 " --> pdb=" O LYS X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 108 through 111 removed outlier: 3.924A pdb=" N TYR X 111 " --> pdb=" O SER X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 108 through 111' Processing helix chain 'X' and resid 116 through 128 removed outlier: 3.748A pdb=" N ALA X 128 " --> pdb=" O ASN X 124 " (cutoff:3.500A) Processing helix chain 'X' and resid 182 through 184 No H-bonds generated for 'chain 'X' and resid 182 through 184' Processing helix chain 'X' and resid 185 through 193 removed outlier: 3.614A pdb=" N ILE X 189 " --> pdb=" O ILE X 185 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 272 Processing helix chain 'X' and resid 281 through 298 removed outlier: 3.718A pdb=" N ARG X 285 " --> pdb=" O THR X 281 " (cutoff:3.500A) Processing helix chain 'X' and resid 313 through 316 Processing helix chain 'X' and resid 317 through 328 removed outlier: 3.510A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 410 removed outlier: 4.439A pdb=" N LEU X 402 " --> pdb=" O SER X 398 " (cutoff:3.500A) Processing helix chain 'X' and resid 411 through 418 Processing helix chain 'X' and resid 418 through 429 Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 459 Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 removed outlier: 3.557A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 106 No H-bonds generated for 'chain 'Y' and resid 104 through 106' Processing helix chain 'Y' and resid 112 through 125 removed outlier: 3.886A pdb=" N ILE Y 125 " --> pdb=" O PHE Y 121 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 181 removed outlier: 4.040A pdb=" N LYS Y 181 " --> pdb=" O ASP Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 205 through 209 Processing helix chain 'Y' and resid 241 through 250 removed outlier: 4.015A pdb=" N ARG Y 250 " --> pdb=" O VAL Y 246 " (cutoff:3.500A) Processing helix chain 'Y' and resid 255 through 260 Processing helix chain 'Y' and resid 266 through 283 removed outlier: 3.602A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 302 through 313 removed outlier: 3.848A pdb=" N ARG Y 311 " --> pdb=" O SER Y 307 " (cutoff:3.500A) Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.934A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 3.898A pdb=" N SER Y 399 " --> pdb=" O SER Y 395 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 Processing helix chain 'Y' and resid 432 through 443 Processing helix chain 'Z' and resid 194 through 232 Processing helix chain 'Z' and resid 238 through 277 removed outlier: 4.241A pdb=" N GLN Z 277 " --> pdb=" O LEU Z 273 " (cutoff:3.500A) Processing helix chain 'Z' and resid 302 through 319 Processing helix chain 'Z' and resid 603 through 615 removed outlier: 4.001A pdb=" N PHE Z 614 " --> pdb=" O ASN Z 610 " (cutoff:3.500A) Processing helix chain 'Z' and resid 615 through 623 removed outlier: 4.446A pdb=" N GLY Z 623 " --> pdb=" O SER Z 619 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 118 through 119 removed outlier: 3.798A pdb=" N ILE B 119 " --> pdb=" O ARG C 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 96 through 98 removed outlier: 6.252A pdb=" N THR C 96 " --> pdb=" O THR E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'M' and resid 717 through 718 removed outlier: 6.510A pdb=" N GLY M 717 " --> pdb=" O LEU M 850 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN M 819 " --> pdb=" O ARG M 847 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LEU M 849 " --> pdb=" O GLN M 819 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET M 821 " --> pdb=" O LEU M 849 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N LEU M 851 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU M 823 " --> pdb=" O LEU M 851 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU M 749 " --> pdb=" O VAL M 822 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N ASP M 824 " --> pdb=" O LEU M 749 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL M 751 " --> pdb=" O ASP M 824 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N HIS M 748 " --> pdb=" O CYS M 799 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL M 801 " --> pdb=" O HIS M 748 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE M 750 " --> pdb=" O VAL M 801 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU M 774 " --> pdb=" O ILE M 800 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N SER M 802 " --> pdb=" O LEU M 774 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N TYR M 776 " --> pdb=" O SER M 802 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 944 through 951 removed outlier: 6.281A pdb=" N VAL M1336 " --> pdb=" O TYR M1367 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N PHE M1369 " --> pdb=" O VAL M1336 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE M1338 " --> pdb=" O PHE M1369 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N SER M1371 " --> pdb=" O PHE M1338 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU M1266 " --> pdb=" O ILE M1337 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA M1265 " --> pdb=" O PHE M1317 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU M1319 " --> pdb=" O ALA M1265 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE M1267 " --> pdb=" O LEU M1319 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET M1290 " --> pdb=" O ILE M1318 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N SER M1320 " --> pdb=" O MET M1290 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU M1292 " --> pdb=" O SER M1320 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 26 through 29 Processing sheet with id=AA6, first strand: chain 'R' and resid 40 through 41 removed outlier: 3.557A pdb=" N TYR R 41 " --> pdb=" O ALA R 33 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA R 33 " --> pdb=" O TYR R 41 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 148 through 151 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 148 through 151 current: chain 'R' and resid 198 through 204 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 207 through 208 current: chain 'R' and resid 384 through 387 Processing sheet with id=AA8, first strand: chain 'R' and resid 287 through 288 Processing sheet with id=AA9, first strand: chain 'S' and resid 6 through 8 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 6 through 8 current: chain 'V' and resid 167 through 171 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 176 through 180 current: chain 'V' and resid 209 through 215 removed outlier: 6.453A pdb=" N VAL V 230 " --> pdb=" O VAL V 212 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 20 through 21 removed outlier: 6.867A pdb=" N THR U 159 " --> pdb=" O VAL U 141 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE U 143 " --> pdb=" O LYS U 157 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LYS U 157 " --> pdb=" O ILE U 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 170 current: chain 'U' and resid 199 through 201 Processing sheet with id=AB2, first strand: chain 'S' and resid 254 through 255 Processing sheet with id=AB3, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB4, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.420A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE T 75 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N SER T 340 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU T 77 " --> pdb=" O SER T 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 130 through 140 removed outlier: 6.704A pdb=" N VAL T 199 " --> pdb=" O VAL T 212 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'T' and resid 144 through 148 removed outlier: 6.635A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AB8, first strand: chain 'T' and resid 394 through 395 removed outlier: 7.157A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'U' and resid 40 through 41 removed outlier: 3.622A pdb=" N SER U 41 " --> pdb=" O MET U 44 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET U 44 " --> pdb=" O SER U 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.759A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'U' and resid 330 through 331 Processing sheet with id=AC3, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.441A pdb=" N CYS V 103 " --> pdb=" O PHE V 309 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N ASP V 311 " --> pdb=" O CYS V 103 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU V 105 " --> pdb=" O ASP V 311 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU V 308 " --> pdb=" O VAL V 337 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ALA V 339 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILE V 310 " --> pdb=" O ALA V 339 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER V 340 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 246 through 248 Processing sheet with id=AC5, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AC6, first strand: chain 'V' and resid 394 through 395 removed outlier: 7.645A pdb=" N GLN V 394 " --> pdb=" O ILE V 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC8, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.336A pdb=" N THR W 99 " --> pdb=" O PHE W 294 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ASP W 296 " --> pdb=" O THR W 99 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE W 101 " --> pdb=" O ASP W 296 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 125 through 148 removed outlier: 5.621A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 199 through 204 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 199 through 204 current: chain 'X' and resid 162 through 172 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'Z' and resid 590 through 595 Processing sheet with id=AD1, first strand: chain 'W' and resid 329 through 331 Processing sheet with id=AD2, first strand: chain 'X' and resid 44 through 45 Processing sheet with id=AD3, first strand: chain 'X' and resid 102 through 106 removed outlier: 3.586A pdb=" N SER X 340 " --> pdb=" O LEU X 77 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 130 through 141 Processing sheet with id=AD5, first strand: chain 'X' and resid 344 through 346 Processing sheet with id=AD6, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.423A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'Y' and resid 40 through 41 Processing sheet with id=AD8, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.149A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 126 through 137 Processing sheet with id=AE1, first strand: chain 'Y' and resid 157 through 161 Processing sheet with id=AE2, first strand: chain 'Y' and resid 329 through 331 1662 hydrogen bonds defined for protein. 4845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 546 hydrogen bond angles 0 basepair planarities 111 basepair parallelities 189 stacking parallelities Total time for adding SS restraints: 11.95 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10683 1.33 - 1.46: 8997 1.46 - 1.58: 22743 1.58 - 1.70: 494 1.70 - 1.82: 199 Bond restraints: 43116 Sorted by residual: bond pdb=" C1' DT I 14 " pdb=" N1 DT I 14 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.49e+01 bond pdb=" C1' DT J -23 " pdb=" N1 DT J -23 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.18e+01 bond pdb=" C3' DC I -38 " pdb=" C2' DC I -38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA I -9 " pdb=" C2' DA I -9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.72e+00 ... (remaining 43111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 58929 3.04 - 6.09: 371 6.09 - 9.13: 35 9.13 - 12.17: 5 12.17 - 15.22: 6 Bond angle restraints: 59346 Sorted by residual: angle pdb=" O4' DC J -27 " pdb=" C1' DC J -27 " pdb=" N1 DC J -27 " ideal model delta sigma weight residual 108.00 112.10 -4.10 7.00e-01 2.04e+00 3.43e+01 angle pdb=" C THR Z 595 " pdb=" N LEU Z 596 " pdb=" CA LEU Z 596 " ideal model delta sigma weight residual 121.70 132.20 -10.50 1.80e+00 3.09e-01 3.41e+01 angle pdb=" C LYS P 218 " pdb=" N ARG P 219 " pdb=" CA ARG P 219 " ideal model delta sigma weight residual 121.70 130.66 -8.96 1.80e+00 3.09e-01 2.48e+01 angle pdb=" CB MET M 871 " pdb=" CG MET M 871 " pdb=" SD MET M 871 " ideal model delta sigma weight residual 112.70 127.42 -14.72 3.00e+00 1.11e-01 2.41e+01 angle pdb=" N3 DT I 14 " pdb=" C4 DT I 14 " pdb=" O4 DT I 14 " ideal model delta sigma weight residual 119.90 122.79 -2.89 6.00e-01 2.78e+00 2.32e+01 ... (remaining 59341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.21: 22817 29.21 - 58.42: 2631 58.42 - 87.63: 210 87.63 - 116.83: 5 116.83 - 146.04: 2 Dihedral angle restraints: 25665 sinusoidal: 11793 harmonic: 13872 Sorted by residual: dihedral pdb=" CA MET M 871 " pdb=" C MET M 871 " pdb=" N PRO M 872 " pdb=" CA PRO M 872 " ideal model delta harmonic sigma weight residual 180.00 -145.28 -34.72 0 5.00e+00 4.00e-02 4.82e+01 dihedral pdb=" CA THR P 236 " pdb=" C THR P 236 " pdb=" N THR P 237 " pdb=" CA THR P 237 " ideal model delta harmonic sigma weight residual 180.00 -149.07 -30.93 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" O1B ADP V 501 " pdb=" O3A ADP V 501 " pdb=" PB ADP V 501 " pdb=" PA ADP V 501 " ideal model delta sinusoidal sigma weight residual -60.00 -152.29 92.29 1 2.00e+01 2.50e-03 2.50e+01 ... (remaining 25662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 5613 0.052 - 0.105: 1131 0.105 - 0.157: 195 0.157 - 0.210: 9 0.210 - 0.262: 2 Chirality restraints: 6950 Sorted by residual: chirality pdb=" CG LEU C 58 " pdb=" CB LEU C 58 " pdb=" CD1 LEU C 58 " pdb=" CD2 LEU C 58 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE P 227 " pdb=" CA ILE P 227 " pdb=" CG1 ILE P 227 " pdb=" CG2 ILE P 227 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU M1026 " pdb=" CB LEU M1026 " pdb=" CD1 LEU M1026 " pdb=" CD2 LEU M1026 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.07e-01 ... (remaining 6947 not shown) Planarity restraints: 6736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET M 871 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO M 872 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO M 872 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO M 872 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.75e+00 pdb=" N PRO A 121 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS M 995 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO M 996 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO M 996 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO M 996 " -0.031 5.00e-02 4.00e+02 ... (remaining 6733 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 426 2.57 - 3.15: 33935 3.15 - 3.73: 70124 3.73 - 4.32: 89598 4.32 - 4.90: 144149 Nonbonded interactions: 338232 Sorted by model distance: nonbonded pdb=" F1 BEF R 502 " pdb="MG MG R 503 " model vdw 1.982 2.120 nonbonded pdb=" O3B ADP V 501 " pdb="MG MG V 502 " model vdw 1.998 2.170 nonbonded pdb=" O2B ADP Y 501 " pdb="MG MG Y 502 " model vdw 2.007 2.170 nonbonded pdb=" O2B ADP T 501 " pdb="MG MG T 502 " model vdw 2.010 2.170 nonbonded pdb=" O2B ADP X 501 " pdb="MG MG X 502 " model vdw 2.019 2.170 ... (remaining 338227 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 or (resid 45 and (name N or name CA or name C or name O \ or name CB )) or resid 46 through 47 or (resid 48 and (name N or name CA or nam \ e C or name O or name CB )) or resid 49 through 58 or (resid 59 and (name N or n \ ame CA or name C or name O or name CB )) or resid 60 through 63 or (resid 64 and \ (name N or name CA or name C or name O or name CB )) or resid 65 through 72 or \ (resid 73 and (name N or name CA or name C or name O or name CB )) or resid 74 t \ hrough 82 or (resid 83 and (name N or name CA or name C or name O or name CB )) \ or resid 84 or (resid 85 and (name N or name CA or name C or name O or name CB ) \ ) or resid 86 through 124 or (resid 125 and (name N or name CA or name C or name \ O or name CB )) or resid 126 through 132 or (resid 133 and (name N or name CA o \ r name C or name O or name CB )))) selection = (chain 'B' and resid 44 through 133) } ncs_group { reference = (chain 'T' and (resid 22 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 41 or (resid 42 and (name N or nam \ e CA or name C or name O or name CB )) or resid 43 through 149 or (resid 150 and \ (name N or name CA or name C or name O or name CB )) or resid 166 through 170 o \ r (resid 171 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 72 through 186 or (resid 187 and (name N or name CA or name C or name O or name \ CB )) or resid 188 through 212 or resid 214 through 220 or (resid 221 through 22 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 224 through \ 259 or (resid 260 and (name N or name CA or name C or name O or name CB )) or re \ sid 261 through 268 or (resid 269 and (name N or name CA or name C or name O or \ name CB )) or resid 270 or (resid 271 and (name N or name CA or name C or name O \ or name CB )) or resid 272 or (resid 273 and (name N or name CA or name C or na \ me O or name CB )) or resid 274 through 275 or (resid 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 502)) selection = (chain 'V' and (resid 22 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 141 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 149 or (resid 150 \ and (name N or name CA or name C or name O or name CB )) or resid 166 through 19 \ 1 or (resid 192 through 193 and (name N or name CA or name C or name O or name C \ B )) or resid 194 through 212 or resid 214 through 226 or (resid 227 through 228 \ and (name N or name CA or name C or name O or name CB )) or resid 229 through 2 \ 57 or (resid 258 and (name N or name CA or name C or name O or name CB )) or res \ id 259 through 268 or (resid 269 and (name N or name CA or name C or name O or n \ ame CB )) or resid 270 or (resid 271 and (name N or name CA or name C or name O \ or name CB )) or resid 272 or (resid 273 and (name N or name CA or name C or nam \ e O or name CB )) or resid 274 through 275 or (resid 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 502)) selection = (chain 'X' and (resid 22 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 141 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 150 or resid 166 t \ hrough 170 or (resid 171 and (name N or name CA or name C or name O or name CB ) \ ) or resid 172 through 186 or (resid 187 and (name N or name CA or name C or nam \ e O or name CB )) or resid 188 through 190 or (resid 191 through 193 and (name N \ or name CA or name C or name O or name CB )) or resid 194 through 220 or (resid \ 221 through 223 and (name N or name CA or name C or name O or name CB )) or res \ id 224 through 226 or (resid 227 through 228 and (name N or name CA or name C or \ name O or name CB )) or resid 229 through 257 or (resid 258 and (name N or name \ CA or name C or name O or name CB )) or resid 259 or (resid 260 and (name N or \ name CA or name C or name O or name CB )) or resid 261 through 462 or resid 501 \ through 502)) } ncs_group { reference = (chain 'U' and (resid 15 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 136 or (resid 137 and (name N or n \ ame CA or name C or name O or name CB )) or resid 138 or (resid 139 and (name N \ or name CA or name C or name O or name CB )) or resid 140 through 143 or (resid \ 144 and (name N or name CA or name C or name O or name CB )) or resid 145 or (re \ sid 146 and (name N or name CA or name C or name O or name CB )) or (resid 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 155 and (name N or name CA or name C or name O or name CB \ )) or resid 156 or (resid 157 and (name N or name CA or name C or name O or nam \ e CB )) or resid 158 through 169 or (resid 170 and (name N or name CA or name C \ or name O or name CB )) or resid 171 through 180 or (resid 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 203 or (resid 204 a \ nd (name N or name CA or name C or name O or name CB )) or resid 205 through 207 \ or resid 221 through 222 or (resid 223 and (name N or name CA or name C or name \ O or name CB )) or resid 224 through 225 or (resid 226 and (name N or name CA o \ r name C or name O or name CB )) or resid 227 through 228 or (resid 229 and (nam \ e N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 and \ (name N or name CA or name C or name O or name CB )) or resid 232 through 281 or \ (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 28 \ 3 through 418 or (resid 419 and (name N or name CA or name C or name O or name C \ B )) or resid 420 through 421 or (resid 422 and (name N or name CA or name C or \ name O or name CB )) or resid 423 through 459 or resid 501 through 502)) selection = (chain 'W' and (resid 15 through 32 or (resid 33 and (name N or name CA or name \ C or name O or name CB )) or resid 34 through 143 or (resid 144 and (name N or n \ ame CA or name C or name O or name CB )) or resid 145 or (resid 146 and (name N \ or name CA or name C or name O or name CB )) or (resid 150 and (name N or name C \ A or name C or name O or name CB )) or resid 151 through 152 or (resid 153 throu \ gh 155 and (name N or name CA or name C or name O or name CB )) or resid 156 or \ (resid 157 and (name N or name CA or name C or name O or name CB )) or resid 158 \ through 169 or (resid 170 and (name N or name CA or name C or name O or name CB \ )) or resid 171 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 228 or (resid 229 and ( \ name N or name CA or name C or name O or name CB )) or resid 230 or (resid 231 a \ nd (name N or name CA or name C or name O or name CB )) or resid 232 through 418 \ or (resid 419 and (name N or name CA or name C or name O or name CB )) or resid \ 420 through 421 or (resid 422 and (name N or name CA or name C or name O or nam \ e CB )) or resid 423 through 502)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 203 or (resid 204 and (name N o \ r name CA or name C or name O or name CB )) or resid 205 through 207 or resid 22 \ 1 through 222 or (resid 223 and (name N or name CA or name C or name O or name C \ B )) or resid 224 through 225 or (resid 226 and (name N or name CA or name C or \ name O or name CB )) or resid 227 through 281 or (resid 282 and (name N or name \ CA or name C or name O or name CB )) or resid 283 through 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.130 Process input model: 52.410 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 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 0.796 43125 Z= 0.466 Angle : 0.684 15.215 59349 Z= 0.434 Chirality : 0.043 0.262 6950 Planarity : 0.004 0.103 6736 Dihedral : 21.472 146.042 16681 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.66 % Favored : 94.05 % Rotamer: Outliers : 0.35 % Allowed : 33.43 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 4737 helix: 1.06 (0.11), residues: 2216 sheet: 0.06 (0.21), residues: 638 loop : -1.77 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 116 TYR 0.026 0.001 TYR V 201 PHE 0.033 0.001 PHE G 68 TRP 0.020 0.001 TRP Z 309 HIS 0.006 0.001 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.27 (43116) covalent geometry : angle 0.68424 / 0.43 (59346) hydrogen bonds : bond 0.13388 / 9.16 ( 1947) hydrogen bonds : angle 5.22857 / 3.65 ( 5391) metal coordination : bond 0.00571 / 0.46 ( 7) metal coordination : angle 1.43535 / 0.54 ( 3) Misc. bond : bond 0.56310 / 35.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 829 time to evaluate : 0.987 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: A 49 ARG cc_start: 0.7697 (mmm160) cc_final: 0.7428 (mpt180) REVERT: B 76 GLN cc_start: 0.9070 (pt0) cc_final: 0.8562 (pp30) REVERT: B 112 ILE cc_start: 0.8881 (tp) cc_final: 0.8633 (tt) REVERT: C 72 TYR cc_start: 0.8647 (t80) cc_final: 0.8153 (t80) REVERT: D 61 PHE cc_start: 0.8518 (t80) cc_final: 0.8219 (t80) REVERT: G 54 ASP cc_start: 0.8394 (p0) cc_final: 0.8154 (t0) REVERT: M 734 LEU cc_start: 0.8600 (tp) cc_final: 0.8113 (tp) REVERT: M 1053 ASP cc_start: 0.8403 (p0) cc_final: 0.7876 (p0) REVERT: M 1118 MET cc_start: 0.8035 (tpp) cc_final: 0.7449 (mtm) REVERT: M 1121 PHE cc_start: 0.8609 (t80) cc_final: 0.8063 (m-80) REVERT: M 1124 MET cc_start: 0.8047 (tmm) cc_final: 0.7756 (tpt) REVERT: M 1276 ASP cc_start: 0.8353 (p0) cc_final: 0.7597 (p0) REVERT: P 238 LEU cc_start: 0.8978 (tp) cc_final: 0.8631 (mt) REVERT: P 240 LYS cc_start: 0.8575 (tptm) cc_final: 0.7927 (tptt) REVERT: P 244 ASP cc_start: 0.8551 (m-30) cc_final: 0.8040 (m-30) REVERT: P 258 LEU cc_start: 0.9220 (mt) cc_final: 0.8980 (mt) REVERT: R 92 LYS cc_start: 0.5346 (pttp) cc_final: 0.4534 (mmtt) REVERT: R 123 TYR cc_start: 0.2989 (t80) cc_final: 0.2749 (m-80) REVERT: R 199 TRP cc_start: 0.6567 (m100) cc_final: 0.5988 (t60) REVERT: R 201 ILE cc_start: 0.8302 (tt) cc_final: 0.8038 (tt) REVERT: R 211 LYS cc_start: 0.5403 (mmmt) cc_final: 0.4802 (tmtt) REVERT: R 332 GLU cc_start: 0.7594 (tp30) cc_final: 0.7085 (mp0) REVERT: S 234 TYR cc_start: 0.5601 (m-80) cc_final: 0.4425 (m-80) REVERT: U 215 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6379 (mtt) REVERT: U 416 ASN cc_start: 0.7606 (p0) cc_final: 0.7400 (p0) REVERT: V 70 MET cc_start: 0.7692 (mmm) cc_final: 0.7377 (mmp) REVERT: V 269 MET cc_start: 0.8767 (ttm) cc_final: 0.8432 (ttp) REVERT: Y 95 ASP cc_start: 0.5590 (t0) cc_final: 0.5294 (t0) REVERT: Y 218 ASP cc_start: 0.8387 (p0) cc_final: 0.8106 (p0) REVERT: Z 196 ARG cc_start: 0.4103 (ttp80) cc_final: 0.3882 (ptt-90) REVERT: Z 200 MET cc_start: 0.0217 (OUTLIER) cc_final: -0.0030 (tpp) REVERT: Z 260 LYS cc_start: 0.8053 (tppt) cc_final: 0.7581 (ptpt) REVERT: Z 263 GLU cc_start: 0.6877 (pt0) cc_final: 0.6224 (tp30) REVERT: Z 317 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8057 (p0) REVERT: Z 321 LYS cc_start: 0.6089 (mmtm) cc_final: 0.5577 (mmtp) REVERT: Z 616 ASP cc_start: 0.4632 (t0) cc_final: 0.4142 (p0) outliers start: 14 outliers final: 2 residues processed: 836 average time/residue: 0.2762 time to fit residues: 367.8704 Evaluate side-chains 424 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 419 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain R residue 241 GLU Chi-restraints excluded: chain U residue 215 MET Chi-restraints excluded: chain Z residue 200 MET Chi-restraints excluded: chain Z residue 317 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 0.2980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 810 GLN M 984 ASN M 994 ASN M1329 ASN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 280 GLN R 324 GLN R 402 GLN ** W 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 94 GLN X 190 GLN ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.092644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.069145 restraints weight = 209428.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.069929 restraints weight = 113904.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.069930 restraints weight = 63717.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.070125 restraints weight = 56257.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.070148 restraints weight = 48146.753| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 43125 Z= 0.144 Angle : 0.687 13.194 59349 Z= 0.355 Chirality : 0.044 0.257 6950 Planarity : 0.004 0.091 6736 Dihedral : 20.529 146.727 7800 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.38 % Favored : 94.32 % Rotamer: Outliers : 3.43 % Allowed : 31.01 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.12), residues: 4737 helix: 1.05 (0.11), residues: 2244 sheet: 0.03 (0.20), residues: 638 loop : -1.82 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 375 TYR 0.023 0.001 TYR G 45 PHE 0.025 0.001 PHE S 19 TRP 0.036 0.001 TRP M 837 HIS 0.013 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (43116) covalent geometry : angle 0.68709 / 0.36 (59346) hydrogen bonds : bond 0.05324 / 3.56 ( 1947) hydrogen bonds : angle 4.41975 / 3.11 ( 5391) metal coordination : bond 0.00688 / 0.55 ( 7) metal coordination : angle 1.65237 / 0.80 ( 3) Misc. bond : bond 0.00082 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 446 time to evaluate : 1.760 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: A 49 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7485 (mpt180) REVERT: A 97 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8141 (mt-10) REVERT: B 112 ILE cc_start: 0.9060 (tp) cc_final: 0.8819 (tt) REVERT: E 58 TYR cc_start: 0.8027 (t80) cc_final: 0.7328 (t80) REVERT: E 108 VAL cc_start: 0.7677 (OUTLIER) cc_final: 0.7427 (m) REVERT: G 50 GLN cc_start: 0.8316 (pp30) cc_final: 0.8107 (pp30) REVERT: G 51 THR cc_start: 0.6160 (t) cc_final: 0.5054 (t) REVERT: G 52 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7189 (m90) REVERT: G 54 ASP cc_start: 0.8460 (p0) cc_final: 0.8215 (t0) REVERT: G 116 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6946 (tt0) REVERT: M 734 LEU cc_start: 0.8492 (tp) cc_final: 0.8142 (tp) REVERT: M 760 TRP cc_start: 0.9087 (m100) cc_final: 0.8777 (m100) REVERT: M 871 MET cc_start: 0.8102 (tmm) cc_final: 0.7648 (tmm) REVERT: M 1053 ASP cc_start: 0.8768 (p0) cc_final: 0.8283 (p0) REVERT: M 1106 TYR cc_start: 0.7468 (p90) cc_final: 0.7108 (p90) REVERT: M 1118 MET cc_start: 0.7975 (tpp) cc_final: 0.7355 (mtm) REVERT: M 1121 PHE cc_start: 0.8834 (t80) cc_final: 0.8082 (m-80) REVERT: M 1211 LEU cc_start: 0.8612 (tt) cc_final: 0.8360 (mt) REVERT: M 1273 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8679 (mmmt) REVERT: M 1276 ASP cc_start: 0.8572 (p0) cc_final: 0.8170 (p0) REVERT: M 1390 ASP cc_start: 0.6243 (t0) cc_final: 0.5923 (t70) REVERT: P 240 LYS cc_start: 0.8596 (tptm) cc_final: 0.7930 (ttmt) REVERT: P 244 ASP cc_start: 0.8762 (m-30) cc_final: 0.8551 (m-30) REVERT: R 92 LYS cc_start: 0.5336 (pttp) cc_final: 0.4330 (mmtt) REVERT: R 123 TYR cc_start: 0.4113 (t80) cc_final: 0.2769 (m-80) REVERT: R 199 TRP cc_start: 0.6407 (m100) cc_final: 0.5627 (t60) REVERT: R 211 LYS cc_start: 0.5015 (mmmt) cc_final: 0.4499 (tmtt) REVERT: R 239 MET cc_start: 0.6629 (tmm) cc_final: 0.6270 (tmm) REVERT: R 332 GLU cc_start: 0.7627 (tp30) cc_final: 0.7368 (mp0) REVERT: S 102 PHE cc_start: 0.7799 (t80) cc_final: 0.7374 (t80) REVERT: S 115 ASN cc_start: 0.5661 (OUTLIER) cc_final: 0.5432 (t0) REVERT: S 135 THR cc_start: 0.4818 (OUTLIER) cc_final: 0.4562 (t) REVERT: S 223 ASN cc_start: 0.2853 (OUTLIER) cc_final: 0.2615 (m110) REVERT: S 234 TYR cc_start: 0.5405 (m-80) cc_final: 0.4340 (m-80) REVERT: T 234 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8278 (tppt) REVERT: U 204 ARG cc_start: 0.6692 (tpp-160) cc_final: 0.6017 (mmm160) REVERT: U 416 ASN cc_start: 0.7947 (p0) cc_final: 0.7674 (p0) REVERT: W 190 ILE cc_start: 0.8727 (mm) cc_final: 0.8472 (tp) REVERT: X 190 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: X 224 LEU cc_start: 0.6329 (OUTLIER) cc_final: 0.6059 (tt) REVERT: Y 95 ASP cc_start: 0.6278 (t0) cc_final: 0.5971 (t0) REVERT: Y 115 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7855 (tp30) REVERT: Z 196 ARG cc_start: 0.4287 (ttp80) cc_final: 0.3941 (ptt-90) REVERT: Z 260 LYS cc_start: 0.8222 (tppt) cc_final: 0.7551 (ptpt) REVERT: Z 263 GLU cc_start: 0.6962 (pt0) cc_final: 0.6421 (tp30) REVERT: Z 317 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8047 (p0) REVERT: Z 321 LYS cc_start: 0.6181 (mmtm) cc_final: 0.5607 (mmtp) outliers start: 136 outliers final: 41 residues processed: 556 average time/residue: 0.2653 time to fit residues: 243.3392 Evaluate side-chains 419 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 367 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1104 PHE Chi-restraints excluded: chain M residue 1318 ILE Chi-restraints excluded: chain M residue 1328 ILE Chi-restraints excluded: chain M residue 1366 ILE Chi-restraints excluded: chain R residue 238 MET Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 408 SER Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 115 ASN Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 234 LYS Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 162 THR Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 296 ASP Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 438 LYS Chi-restraints excluded: chain X residue 190 GLN Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain X residue 316 LEU Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 381 SER Chi-restraints excluded: chain Z residue 317 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 251 optimal weight: 0.9980 chunk 280 optimal weight: 6.9990 chunk 245 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 321 optimal weight: 0.0970 chunk 190 optimal weight: 4.9990 chunk 125 optimal weight: 0.9990 chunk 241 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 838 GLN M 984 ASN M1280 GLN M1352 GLN P 255 ASN P 262 ASN P 291 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 270 HIS S 115 ASN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 451 GLN ** W 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 289 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.091292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.067627 restraints weight = 210534.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.068021 restraints weight = 118825.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.068378 restraints weight = 74674.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.068367 restraints weight = 55735.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068436 restraints weight = 54467.998| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 43125 Z= 0.150 Angle : 0.660 11.020 59349 Z= 0.342 Chirality : 0.044 0.364 6950 Planarity : 0.004 0.097 6736 Dihedral : 20.500 142.733 7789 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.28 % Favored : 94.43 % Rotamer: Outliers : 3.84 % Allowed : 29.34 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 4737 helix: 1.10 (0.11), residues: 2247 sheet: 0.10 (0.20), residues: 648 loop : -1.80 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 92 TYR 0.025 0.001 TYR G 86 PHE 0.017 0.001 PHE G 68 TRP 0.033 0.001 TRP M 837 HIS 0.022 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (43116) covalent geometry : angle 0.65998 / 0.34 (59346) hydrogen bonds : bond 0.04817 / 3.23 ( 1947) hydrogen bonds : angle 4.20942 / 2.96 ( 5391) metal coordination : bond 0.00930 / 0.74 ( 7) metal coordination : angle 1.40229 / 0.78 ( 3) Misc. bond : bond 0.00172 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 393 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7416 (mpt180) REVERT: A 97 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7903 (mt-10) REVERT: A 106 ASP cc_start: 0.9207 (t0) cc_final: 0.8858 (t0) REVERT: B 112 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8842 (tt) REVERT: C 53 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7132 (mt-10) REVERT: C 92 ARG cc_start: 0.7443 (mtm180) cc_final: 0.7111 (mtt90) REVERT: E 58 TYR cc_start: 0.8041 (t80) cc_final: 0.7179 (t80) REVERT: E 108 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7590 (m) REVERT: G 49 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8817 (mttt) REVERT: G 52 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.7253 (m-70) REVERT: M 760 TRP cc_start: 0.9146 (m100) cc_final: 0.8808 (m100) REVERT: M 871 MET cc_start: 0.8072 (tmm) cc_final: 0.7623 (tmm) REVERT: M 1053 ASP cc_start: 0.8885 (p0) cc_final: 0.8495 (p0) REVERT: M 1118 MET cc_start: 0.7973 (tpp) cc_final: 0.7534 (ttm) REVERT: M 1121 PHE cc_start: 0.8842 (t80) cc_final: 0.8037 (m-80) REVERT: M 1273 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8663 (mmmt) REVERT: M 1276 ASP cc_start: 0.8574 (p0) cc_final: 0.8052 (p0) REVERT: M 1387 ARG cc_start: 0.7172 (tpp-160) cc_final: 0.6780 (tpp-160) REVERT: P 240 LYS cc_start: 0.8651 (tptm) cc_final: 0.8087 (tttp) REVERT: P 244 ASP cc_start: 0.8774 (m-30) cc_final: 0.8434 (m-30) REVERT: P 262 ASN cc_start: 0.8511 (m-40) cc_final: 0.8256 (m-40) REVERT: R 92 LYS cc_start: 0.4922 (pttp) cc_final: 0.3841 (mmtt) REVERT: R 106 MET cc_start: 0.5019 (ppp) cc_final: 0.4704 (ppp) REVERT: R 123 TYR cc_start: 0.4246 (t80) cc_final: 0.2879 (m-80) REVERT: R 199 TRP cc_start: 0.6445 (m100) cc_final: 0.5502 (t60) REVERT: R 211 LYS cc_start: 0.4887 (mmmt) cc_final: 0.4463 (tmtt) REVERT: R 239 MET cc_start: 0.6444 (tmm) cc_final: 0.6203 (tmm) REVERT: S 102 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7337 (t80) REVERT: S 110 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7402 (t80) REVERT: S 135 THR cc_start: 0.4611 (OUTLIER) cc_final: 0.4390 (t) REVERT: S 234 TYR cc_start: 0.5214 (m-80) cc_final: 0.4024 (m-80) REVERT: T 112 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8369 (p) REVERT: T 234 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8706 (tppt) REVERT: T 268 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7337 (tmm) REVERT: U 215 MET cc_start: 0.5594 (mtt) cc_final: 0.4302 (ptp) REVERT: U 416 ASN cc_start: 0.7933 (p0) cc_final: 0.7519 (p0) REVERT: V 344 MET cc_start: 0.8394 (mmm) cc_final: 0.8123 (mmm) REVERT: W 165 MET cc_start: 0.7968 (mpp) cc_final: 0.7738 (mpp) REVERT: W 190 ILE cc_start: 0.8884 (mm) cc_final: 0.8629 (tp) REVERT: Y 23 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7814 (p90) REVERT: Y 95 ASP cc_start: 0.6405 (t0) cc_final: 0.6089 (t0) REVERT: Y 115 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8078 (tp30) REVERT: Y 175 MET cc_start: 0.6053 (mmm) cc_final: 0.5778 (mmm) REVERT: Z 196 ARG cc_start: 0.4380 (ttp80) cc_final: 0.3867 (ptt-90) REVERT: Z 260 LYS cc_start: 0.8165 (tppt) cc_final: 0.7639 (ptpt) REVERT: Z 263 GLU cc_start: 0.7055 (pt0) cc_final: 0.6480 (tp30) REVERT: Z 317 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8171 (p0) REVERT: Z 321 LYS cc_start: 0.6323 (mmtm) cc_final: 0.5742 (mmtp) REVERT: Z 595 THR cc_start: 0.6766 (OUTLIER) cc_final: 0.6378 (m) outliers start: 152 outliers final: 66 residues processed: 510 average time/residue: 0.2616 time to fit residues: 221.5318 Evaluate side-chains 426 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 346 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 1009 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1067 CYS Chi-restraints excluded: chain M residue 1104 PHE Chi-restraints excluded: chain M residue 1178 ASP Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1318 ILE Chi-restraints excluded: chain M residue 1352 GLN Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain R residue 107 THR Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 102 PHE Chi-restraints excluded: chain S residue 110 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 234 LYS Chi-restraints excluded: chain T residue 268 MET Chi-restraints excluded: chain T residue 359 VAL Chi-restraints excluded: chain U residue 82 THR Chi-restraints excluded: chain U residue 84 LEU Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 438 LYS Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 27 THR Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 381 SER Chi-restraints excluded: chain Z residue 312 GLN Chi-restraints excluded: chain Z residue 317 ASP Chi-restraints excluded: chain Z residue 588 LEU Chi-restraints excluded: chain Z residue 595 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 293 optimal weight: 0.9990 chunk 400 optimal weight: 4.9990 chunk 361 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 126 optimal weight: 0.9990 chunk 481 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 325 optimal weight: 0.4980 chunk 223 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 324 GLN S 97 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN X 417 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.090803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.067363 restraints weight = 208454.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.067853 restraints weight = 109926.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.067945 restraints weight = 62840.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.067988 restraints weight = 67784.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.067982 restraints weight = 53143.282| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 43125 Z= 0.137 Angle : 0.640 10.694 59349 Z= 0.330 Chirality : 0.043 0.357 6950 Planarity : 0.004 0.090 6736 Dihedral : 20.498 143.032 7789 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.07 % Favored : 94.66 % Rotamer: Outliers : 3.31 % Allowed : 29.17 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.12), residues: 4737 helix: 1.16 (0.11), residues: 2257 sheet: 0.11 (0.20), residues: 636 loop : -1.75 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Z 306 TYR 0.015 0.001 TYR M1367 PHE 0.018 0.001 PHE T 125 TRP 0.019 0.001 TRP M 837 HIS 0.020 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (43116) covalent geometry : angle 0.64039 / 0.33 (59346) hydrogen bonds : bond 0.04510 / 3.02 ( 1947) hydrogen bonds : angle 4.11212 / 2.90 ( 5391) metal coordination : bond 0.00899 / 0.72 ( 7) metal coordination : angle 1.45061 / 0.78 ( 3) Misc. bond : bond 0.00257 / 0.16 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 364 time to evaluate : 1.700 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 49 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7482 (mpt180) REVERT: A 73 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7764 (mt-10) REVERT: A 94 GLU cc_start: 0.7790 (tp30) cc_final: 0.7589 (tp30) REVERT: A 97 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7882 (mt-10) REVERT: A 106 ASP cc_start: 0.9223 (t0) cc_final: 0.8886 (t0) REVERT: B 112 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8844 (tt) REVERT: E 58 TYR cc_start: 0.8053 (t80) cc_final: 0.7262 (t80) REVERT: E 108 VAL cc_start: 0.7871 (OUTLIER) cc_final: 0.7638 (m) REVERT: G 49 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8754 (mmtt) REVERT: G 51 THR cc_start: 0.6201 (t) cc_final: 0.5840 (t) REVERT: G 52 HIS cc_start: 0.7648 (OUTLIER) cc_final: 0.7265 (m-70) REVERT: G 119 ARG cc_start: 0.8427 (ptm-80) cc_final: 0.8215 (ppt170) REVERT: M 760 TRP cc_start: 0.9167 (m100) cc_final: 0.8845 (m100) REVERT: M 820 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7931 (t80) REVERT: M 871 MET cc_start: 0.7960 (tmm) cc_final: 0.7595 (tmm) REVERT: M 915 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.8110 (mmmm) REVERT: M 965 MET cc_start: 0.8497 (tpp) cc_final: 0.8260 (tpt) REVERT: M 1053 ASP cc_start: 0.8890 (p0) cc_final: 0.8542 (p0) REVERT: M 1106 TYR cc_start: 0.7563 (p90) cc_final: 0.7169 (p90) REVERT: M 1118 MET cc_start: 0.7974 (tpp) cc_final: 0.7528 (ttm) REVERT: M 1121 PHE cc_start: 0.8845 (t80) cc_final: 0.8070 (m-80) REVERT: M 1276 ASP cc_start: 0.8571 (p0) cc_final: 0.7946 (p0) REVERT: M 1387 ARG cc_start: 0.7076 (tpp-160) cc_final: 0.6775 (tpp-160) REVERT: P 240 LYS cc_start: 0.8694 (tptm) cc_final: 0.8140 (tttp) REVERT: P 244 ASP cc_start: 0.8714 (m-30) cc_final: 0.8414 (m-30) REVERT: P 262 ASN cc_start: 0.8569 (m-40) cc_final: 0.8229 (m110) REVERT: P 283 ARG cc_start: 0.8968 (ttp80) cc_final: 0.8718 (ttp80) REVERT: R 92 LYS cc_start: 0.4791 (pttp) cc_final: 0.3699 (mmtt) REVERT: R 106 MET cc_start: 0.4705 (ppp) cc_final: 0.4479 (ppp) REVERT: R 123 TYR cc_start: 0.4200 (t80) cc_final: 0.2911 (m-80) REVERT: R 199 TRP cc_start: 0.6474 (m100) cc_final: 0.5521 (t60) REVERT: R 201 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8406 (tt) REVERT: R 211 LYS cc_start: 0.4898 (mmmt) cc_final: 0.4438 (tmtt) REVERT: S 102 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7500 (t80) REVERT: S 110 PHE cc_start: 0.7609 (OUTLIER) cc_final: 0.7320 (t80) REVERT: S 135 THR cc_start: 0.4703 (OUTLIER) cc_final: 0.4461 (t) REVERT: S 234 TYR cc_start: 0.4553 (m-80) cc_final: 0.4052 (m-80) REVERT: S 235 PHE cc_start: 0.2908 (m-80) cc_final: 0.2355 (m-80) REVERT: T 268 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7292 (tmm) REVERT: U 204 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7640 (tpm170) REVERT: U 215 MET cc_start: 0.5411 (mtt) cc_final: 0.4578 (ptp) REVERT: U 221 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7266 (t80) REVERT: U 416 ASN cc_start: 0.7993 (p0) cc_final: 0.7588 (p0) REVERT: V 344 MET cc_start: 0.8422 (mmm) cc_final: 0.8072 (mmm) REVERT: W 165 MET cc_start: 0.7912 (mpp) cc_final: 0.7661 (mpp) REVERT: W 190 ILE cc_start: 0.8963 (mm) cc_final: 0.8751 (tp) REVERT: Y 95 ASP cc_start: 0.6291 (t0) cc_final: 0.5989 (t0) REVERT: Y 115 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8196 (tp30) REVERT: Y 175 MET cc_start: 0.6430 (mmm) cc_final: 0.6004 (mmm) REVERT: Y 346 ASP cc_start: 0.7927 (p0) cc_final: 0.7673 (p0) REVERT: Z 196 ARG cc_start: 0.4418 (ttp80) cc_final: 0.3937 (ptt-90) REVERT: Z 260 LYS cc_start: 0.8121 (tppt) cc_final: 0.7490 (ptpt) REVERT: Z 263 GLU cc_start: 0.7019 (pt0) cc_final: 0.6427 (tp30) REVERT: Z 317 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8231 (p0) REVERT: Z 321 LYS cc_start: 0.6340 (mmtm) cc_final: 0.5649 (mmtt) outliers start: 131 outliers final: 72 residues processed: 468 average time/residue: 0.2623 time to fit residues: 204.0570 Evaluate side-chains 421 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 335 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 116 GLU Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 843 PHE Chi-restraints excluded: chain M residue 915 LYS Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1104 PHE Chi-restraints excluded: chain M residue 1178 ASP Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1318 ILE Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 324 GLN Chi-restraints excluded: chain R residue 408 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 102 PHE Chi-restraints excluded: chain S residue 110 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 121 LEU Chi-restraints excluded: chain T residue 176 THR Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 268 MET Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 241 LEU Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 438 LYS Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 108 SER Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 322 MET Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Z residue 312 GLN Chi-restraints excluded: chain Z residue 317 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 340 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 323 optimal weight: 0.8980 chunk 299 optimal weight: 1.9990 chunk 369 optimal weight: 5.9990 chunk 483 optimal weight: 2.9990 chunk 356 optimal weight: 0.7980 chunk 491 optimal weight: 0.7980 chunk 353 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 995 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 324 GLN T 256 ASN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.090604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.066815 restraints weight = 207554.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.067496 restraints weight = 102260.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.067559 restraints weight = 58605.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.067653 restraints weight = 51805.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.067644 restraints weight = 47477.689| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43125 Z= 0.122 Angle : 0.631 11.951 59349 Z= 0.322 Chirality : 0.042 0.324 6950 Planarity : 0.004 0.090 6736 Dihedral : 20.471 142.918 7789 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.13 % Favored : 94.60 % Rotamer: Outliers : 3.64 % Allowed : 29.09 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.12), residues: 4737 helix: 1.22 (0.11), residues: 2259 sheet: 0.15 (0.20), residues: 648 loop : -1.75 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 67 TYR 0.014 0.001 TYR Z 597 PHE 0.028 0.001 PHE R 365 TRP 0.014 0.001 TRP M 837 HIS 0.016 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (43116) covalent geometry : angle 0.63094 / 0.32 (59346) hydrogen bonds : bond 0.04329 / 2.88 ( 1947) hydrogen bonds : angle 4.00712 / 2.83 ( 5391) metal coordination : bond 0.00790 / 0.64 ( 7) metal coordination : angle 1.50026 / 0.85 ( 3) Misc. bond : bond 0.00100 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 359 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7369 (mpt180) REVERT: A 97 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7923 (mt-10) REVERT: A 106 ASP cc_start: 0.9324 (t0) cc_final: 0.8971 (t0) REVERT: B 112 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8785 (tt) REVERT: E 58 TYR cc_start: 0.8009 (t80) cc_final: 0.7207 (t80) REVERT: E 108 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7654 (m) REVERT: G 49 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8552 (mmtt) REVERT: G 52 HIS cc_start: 0.7557 (OUTLIER) cc_final: 0.7229 (m-70) REVERT: M 760 TRP cc_start: 0.9122 (m100) cc_final: 0.8830 (m100) REVERT: M 820 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7883 (t80) REVERT: M 837 TRP cc_start: 0.7348 (t60) cc_final: 0.7136 (t60) REVERT: M 871 MET cc_start: 0.7979 (tmm) cc_final: 0.7624 (tmm) REVERT: M 915 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8168 (mmmm) REVERT: M 1053 ASP cc_start: 0.8947 (p0) cc_final: 0.8623 (p0) REVERT: M 1118 MET cc_start: 0.7966 (tpp) cc_final: 0.7534 (ttm) REVERT: M 1121 PHE cc_start: 0.8885 (t80) cc_final: 0.8139 (m-80) REVERT: M 1214 MET cc_start: 0.8371 (ptp) cc_final: 0.7746 (ptp) REVERT: M 1387 ARG cc_start: 0.7084 (tpp-160) cc_final: 0.6727 (tpp-160) REVERT: P 240 LYS cc_start: 0.8752 (tptm) cc_final: 0.8191 (tttp) REVERT: P 244 ASP cc_start: 0.8810 (m-30) cc_final: 0.8465 (m-30) REVERT: R 92 LYS cc_start: 0.4587 (pttp) cc_final: 0.3464 (mmtt) REVERT: R 106 MET cc_start: 0.4670 (ppp) cc_final: 0.4466 (ppp) REVERT: R 123 TYR cc_start: 0.4261 (t80) cc_final: 0.2934 (m-80) REVERT: R 199 TRP cc_start: 0.6483 (m100) cc_final: 0.5558 (t60) REVERT: R 211 LYS cc_start: 0.4800 (mmmt) cc_final: 0.4376 (tmtt) REVERT: S 102 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7443 (t80) REVERT: S 110 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7205 (t80) REVERT: S 135 THR cc_start: 0.4658 (OUTLIER) cc_final: 0.4421 (t) REVERT: S 223 ASN cc_start: 0.3059 (OUTLIER) cc_final: 0.2736 (m110) REVERT: S 234 TYR cc_start: 0.4530 (m-80) cc_final: 0.4032 (m-80) REVERT: S 235 PHE cc_start: 0.3048 (m-80) cc_final: 0.2471 (m-80) REVERT: T 125 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8552 (t80) REVERT: T 234 LYS cc_start: 0.8867 (ttmm) cc_final: 0.8646 (tppt) REVERT: T 268 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7477 (tmm) REVERT: U 215 MET cc_start: 0.5437 (mtt) cc_final: 0.4551 (ptp) REVERT: U 221 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7275 (t80) REVERT: U 416 ASN cc_start: 0.8073 (p0) cc_final: 0.7654 (p0) REVERT: V 344 MET cc_start: 0.8553 (mmm) cc_final: 0.8177 (mmm) REVERT: W 165 MET cc_start: 0.7945 (mpp) cc_final: 0.7653 (mpp) REVERT: Y 23 HIS cc_start: 0.8212 (OUTLIER) cc_final: 0.7542 (p90) REVERT: Y 95 ASP cc_start: 0.6297 (t0) cc_final: 0.5985 (t0) REVERT: Y 115 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8275 (tp30) REVERT: Y 175 MET cc_start: 0.6317 (mmm) cc_final: 0.5935 (mmm) REVERT: Y 346 ASP cc_start: 0.7988 (p0) cc_final: 0.7687 (p0) REVERT: Z 196 ARG cc_start: 0.4433 (ttp80) cc_final: 0.3962 (ptt-90) REVERT: Z 216 LYS cc_start: 0.5510 (tptt) cc_final: 0.5268 (tmtt) REVERT: Z 260 LYS cc_start: 0.8089 (tppt) cc_final: 0.7558 (ptpt) REVERT: Z 263 GLU cc_start: 0.7001 (pt0) cc_final: 0.6361 (tp30) REVERT: Z 313 LEU cc_start: 0.9353 (tp) cc_final: 0.8946 (pp) REVERT: Z 321 LYS cc_start: 0.6370 (mmtm) cc_final: 0.5674 (mmtt) outliers start: 144 outliers final: 84 residues processed: 475 average time/residue: 0.2574 time to fit residues: 204.8397 Evaluate side-chains 426 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 327 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 843 PHE Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 915 LYS Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 988 GLN Chi-restraints excluded: chain M residue 1009 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1104 PHE Chi-restraints excluded: chain M residue 1178 ASP Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1318 ILE Chi-restraints excluded: chain M residue 1328 ILE Chi-restraints excluded: chain M residue 1357 ARG Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain P residue 287 LEU Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 324 GLN Chi-restraints excluded: chain R residue 408 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 102 PHE Chi-restraints excluded: chain S residue 110 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 268 MET Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 142 GLU Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 316 LEU Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 108 SER Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 423 VAL Chi-restraints excluded: chain Z residue 312 GLN Chi-restraints excluded: chain Z residue 588 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 145 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 406 optimal weight: 0.9990 chunk 221 optimal weight: 0.7980 chunk 214 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 260 optimal weight: 0.7980 chunk 361 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 262 ASN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Z 230 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.090236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066335 restraints weight = 207987.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.067347 restraints weight = 102509.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.066947 restraints weight = 61908.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.067211 restraints weight = 54894.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.067288 restraints weight = 46938.150| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 43125 Z= 0.125 Angle : 0.632 11.805 59349 Z= 0.322 Chirality : 0.042 0.359 6950 Planarity : 0.004 0.088 6736 Dihedral : 20.460 143.022 7787 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.19 % Favored : 94.55 % Rotamer: Outliers : 3.36 % Allowed : 29.32 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.12), residues: 4737 helix: 1.26 (0.11), residues: 2264 sheet: 0.13 (0.20), residues: 648 loop : -1.74 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 78 TYR 0.034 0.001 TYR D 51 PHE 0.018 0.001 PHE R 365 TRP 0.011 0.001 TRP M 837 HIS 0.014 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (43116) covalent geometry : angle 0.63148 / 0.32 (59346) hydrogen bonds : bond 0.04282 / 2.85 ( 1947) hydrogen bonds : angle 3.97103 / 2.81 ( 5391) metal coordination : bond 0.00851 / 0.69 ( 7) metal coordination : angle 1.41632 / 0.80 ( 3) Misc. bond : bond 0.00048 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 343 time to evaluate : 1.464 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: A 49 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7342 (mpt180) REVERT: A 106 ASP cc_start: 0.9302 (t0) cc_final: 0.8914 (t0) REVERT: B 93 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7881 (tm-30) REVERT: B 112 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8763 (tt) REVERT: E 58 TYR cc_start: 0.8052 (t80) cc_final: 0.7191 (t80) REVERT: G 49 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8399 (mmtt) REVERT: G 52 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7184 (m-70) REVERT: G 71 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8704 (p0) REVERT: M 820 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.7847 (t80) REVERT: M 837 TRP cc_start: 0.7336 (t60) cc_final: 0.7125 (t60) REVERT: M 871 MET cc_start: 0.7972 (tmm) cc_final: 0.7627 (tmm) REVERT: M 915 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8151 (mmmm) REVERT: M 965 MET cc_start: 0.8511 (tpp) cc_final: 0.8242 (tpt) REVERT: M 1053 ASP cc_start: 0.8935 (p0) cc_final: 0.8614 (p0) REVERT: M 1106 TYR cc_start: 0.7571 (p90) cc_final: 0.7162 (p90) REVERT: M 1118 MET cc_start: 0.8008 (tpp) cc_final: 0.7567 (ttm) REVERT: M 1121 PHE cc_start: 0.8909 (t80) cc_final: 0.8167 (m-80) REVERT: M 1214 MET cc_start: 0.8242 (ptp) cc_final: 0.8038 (ptp) REVERT: M 1387 ARG cc_start: 0.7153 (tpp-160) cc_final: 0.6775 (tpp-160) REVERT: P 240 LYS cc_start: 0.8791 (tptm) cc_final: 0.8220 (tttp) REVERT: P 244 ASP cc_start: 0.8774 (m-30) cc_final: 0.8465 (m-30) REVERT: P 262 ASN cc_start: 0.8523 (m-40) cc_final: 0.8153 (m110) REVERT: R 92 LYS cc_start: 0.4328 (pttp) cc_final: 0.3204 (mmtt) REVERT: R 106 MET cc_start: 0.4804 (ppp) cc_final: 0.4501 (ppp) REVERT: R 123 TYR cc_start: 0.4204 (t80) cc_final: 0.2867 (m-80) REVERT: R 199 TRP cc_start: 0.6481 (m100) cc_final: 0.5557 (t60) REVERT: R 211 LYS cc_start: 0.4818 (mmmt) cc_final: 0.4368 (tmtt) REVERT: R 284 LEU cc_start: 0.3934 (OUTLIER) cc_final: 0.3732 (pp) REVERT: S 102 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7428 (t80) REVERT: S 110 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7203 (t80) REVERT: S 135 THR cc_start: 0.4644 (OUTLIER) cc_final: 0.4413 (t) REVERT: S 234 TYR cc_start: 0.4770 (m-80) cc_final: 0.4291 (m-80) REVERT: S 235 PHE cc_start: 0.3293 (m-80) cc_final: 0.2707 (m-80) REVERT: T 125 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.8517 (t80) REVERT: U 204 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7734 (mmm160) REVERT: U 215 MET cc_start: 0.5255 (mtt) cc_final: 0.4195 (ptp) REVERT: U 221 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7340 (t80) REVERT: U 416 ASN cc_start: 0.8069 (p0) cc_final: 0.7678 (p0) REVERT: V 344 MET cc_start: 0.8597 (mmm) cc_final: 0.8264 (mmm) REVERT: Y 23 HIS cc_start: 0.8302 (OUTLIER) cc_final: 0.7613 (p90) REVERT: Y 95 ASP cc_start: 0.6241 (t0) cc_final: 0.5943 (t0) REVERT: Y 115 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: Y 175 MET cc_start: 0.6383 (mmm) cc_final: 0.6104 (mmm) REVERT: Y 346 ASP cc_start: 0.8051 (p0) cc_final: 0.7750 (p0) REVERT: Z 196 ARG cc_start: 0.4421 (ttp80) cc_final: 0.3866 (ptt-90) REVERT: Z 260 LYS cc_start: 0.8100 (tppt) cc_final: 0.7565 (ptpt) REVERT: Z 263 GLU cc_start: 0.6942 (pt0) cc_final: 0.6366 (tp30) REVERT: Z 321 LYS cc_start: 0.6472 (mmtm) cc_final: 0.5735 (mmtt) outliers start: 133 outliers final: 87 residues processed: 454 average time/residue: 0.2579 time to fit residues: 195.2443 Evaluate side-chains 420 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 318 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ARG Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 915 LYS Chi-restraints excluded: chain M residue 988 GLN Chi-restraints excluded: chain M residue 1009 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1178 ASP Chi-restraints excluded: chain M residue 1197 LEU Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1318 ILE Chi-restraints excluded: chain M residue 1328 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 400 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 102 PHE Chi-restraints excluded: chain S residue 110 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 224 LEU Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 241 LEU Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain X residue 316 LEU Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 108 SER Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 184 VAL Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 423 VAL Chi-restraints excluded: chain Z residue 312 GLN Chi-restraints excluded: chain Z residue 588 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 280 optimal weight: 0.0000 chunk 6 optimal weight: 0.9990 chunk 63 optimal weight: 40.0000 chunk 307 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 354 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 309 optimal weight: 9.9990 chunk 395 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 141 optimal weight: 8.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1173 ASN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 HIS ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.089592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.063521 restraints weight = 207813.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065042 restraints weight = 102652.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.065940 restraints weight = 64208.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.066512 restraints weight = 47693.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.066845 restraints weight = 39816.767| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 43125 Z= 0.134 Angle : 0.645 14.784 59349 Z= 0.327 Chirality : 0.043 0.319 6950 Planarity : 0.004 0.090 6736 Dihedral : 20.465 142.574 7787 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.28 % Favored : 94.47 % Rotamer: Outliers : 3.56 % Allowed : 29.62 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 4737 helix: 1.32 (0.11), residues: 2258 sheet: 0.12 (0.20), residues: 648 loop : -1.75 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG G 119 TYR 0.019 0.001 TYR D 51 PHE 0.022 0.001 PHE G 68 TRP 0.011 0.001 TRP M 837 HIS 0.012 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (43116) covalent geometry : angle 0.64447 / 0.33 (59346) hydrogen bonds : bond 0.04313 / 2.88 ( 1947) hydrogen bonds : angle 3.95090 / 2.80 ( 5391) metal coordination : bond 0.00940 / 0.76 ( 7) metal coordination : angle 1.51673 / 0.87 ( 3) Misc. bond : bond 0.00055 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 338 time to evaluate : 1.678 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 73 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8112 (pp20) REVERT: A 106 ASP cc_start: 0.9274 (t0) cc_final: 0.8883 (t0) REVERT: B 93 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: B 112 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8786 (tt) REVERT: D 68 ASP cc_start: 0.7973 (p0) cc_final: 0.7632 (p0) REVERT: E 58 TYR cc_start: 0.8069 (t80) cc_final: 0.7777 (t80) REVERT: G 49 LYS cc_start: 0.8662 (mmmt) cc_final: 0.8322 (mmtt) REVERT: G 52 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.7179 (m-70) REVERT: G 71 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8676 (p0) REVERT: G 86 TYR cc_start: 0.5299 (OUTLIER) cc_final: 0.4831 (m-80) REVERT: M 820 TYR cc_start: 0.8830 (OUTLIER) cc_final: 0.7854 (t80) REVERT: M 837 TRP cc_start: 0.7369 (t60) cc_final: 0.7149 (t60) REVERT: M 871 MET cc_start: 0.8106 (tmm) cc_final: 0.7766 (tmm) REVERT: M 915 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8133 (mmmm) REVERT: M 1037 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8401 (mpt-90) REVERT: M 1053 ASP cc_start: 0.8948 (p0) cc_final: 0.8657 (p0) REVERT: M 1106 TYR cc_start: 0.7571 (p90) cc_final: 0.7179 (p90) REVERT: M 1117 ASP cc_start: 0.8696 (m-30) cc_final: 0.8356 (p0) REVERT: M 1118 MET cc_start: 0.8042 (tpp) cc_final: 0.7486 (ttm) REVERT: M 1121 PHE cc_start: 0.8902 (t80) cc_final: 0.8178 (m-80) REVERT: M 1387 ARG cc_start: 0.7236 (tpp-160) cc_final: 0.6822 (tpp-160) REVERT: P 240 LYS cc_start: 0.8773 (tptm) cc_final: 0.8218 (tttp) REVERT: P 244 ASP cc_start: 0.8794 (m-30) cc_final: 0.8482 (m-30) REVERT: R 92 LYS cc_start: 0.4404 (pttp) cc_final: 0.3410 (mmtt) REVERT: R 106 MET cc_start: 0.5256 (ppp) cc_final: 0.4967 (ppp) REVERT: R 123 TYR cc_start: 0.4690 (t80) cc_final: 0.3069 (m-80) REVERT: R 199 TRP cc_start: 0.6377 (m100) cc_final: 0.5456 (t60) REVERT: R 211 LYS cc_start: 0.4416 (mmmt) cc_final: 0.4077 (tmtt) REVERT: S 102 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7683 (t80) REVERT: S 135 THR cc_start: 0.4245 (OUTLIER) cc_final: 0.3987 (t) REVERT: S 223 ASN cc_start: 0.3330 (OUTLIER) cc_final: 0.3060 (m110) REVERT: S 234 TYR cc_start: 0.5019 (m-80) cc_final: 0.4698 (m-80) REVERT: S 235 PHE cc_start: 0.2895 (m-80) cc_final: 0.2382 (m-80) REVERT: T 125 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8464 (t80) REVERT: U 204 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7749 (mmm160) REVERT: U 215 MET cc_start: 0.4848 (mtt) cc_final: 0.3888 (ptp) REVERT: U 221 PHE cc_start: 0.7971 (OUTLIER) cc_final: 0.7305 (t80) REVERT: U 416 ASN cc_start: 0.8196 (p0) cc_final: 0.7828 (p0) REVERT: V 251 ASP cc_start: 0.8965 (m-30) cc_final: 0.8711 (m-30) REVERT: V 344 MET cc_start: 0.8613 (mmm) cc_final: 0.8261 (mmm) REVERT: X 406 MET cc_start: 0.8502 (tpp) cc_final: 0.8066 (tpp) REVERT: Y 23 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.7652 (p90) REVERT: Y 95 ASP cc_start: 0.6311 (t0) cc_final: 0.6036 (t0) REVERT: Y 115 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8393 (tp30) REVERT: Y 175 MET cc_start: 0.6501 (mmm) cc_final: 0.6074 (mmm) REVERT: Y 300 MET cc_start: 0.7949 (mtm) cc_final: 0.7685 (mtm) REVERT: Y 346 ASP cc_start: 0.8173 (p0) cc_final: 0.7853 (p0) REVERT: Z 196 ARG cc_start: 0.4425 (ttp80) cc_final: 0.3981 (ptt-90) REVERT: Z 216 LYS cc_start: 0.5687 (tptt) cc_final: 0.5397 (tmtt) REVERT: Z 260 LYS cc_start: 0.7924 (tppt) cc_final: 0.7372 (ptpt) REVERT: Z 263 GLU cc_start: 0.6825 (pt0) cc_final: 0.6221 (tp30) REVERT: Z 321 LYS cc_start: 0.6446 (mmtm) cc_final: 0.5701 (mmtt) outliers start: 141 outliers final: 94 residues processed: 456 average time/residue: 0.2533 time to fit residues: 192.9053 Evaluate side-chains 427 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 318 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 58 SER Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 915 LYS Chi-restraints excluded: chain M residue 988 GLN Chi-restraints excluded: chain M residue 1009 VAL Chi-restraints excluded: chain M residue 1037 ARG Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1104 PHE Chi-restraints excluded: chain M residue 1141 ILE Chi-restraints excluded: chain M residue 1178 ASP Chi-restraints excluded: chain M residue 1318 ILE Chi-restraints excluded: chain M residue 1328 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 408 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 102 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain S residue 223 ASN Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 241 LEU Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain X residue 316 LEU Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 108 SER Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 184 VAL Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 417 THR Chi-restraints excluded: chain Y residue 423 VAL Chi-restraints excluded: chain Y residue 433 SER Chi-restraints excluded: chain Z residue 312 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 261 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 1 optimal weight: 0.0370 chunk 460 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 30.0000 chunk 242 optimal weight: 1.9990 chunk 482 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 231 optimal weight: 9.9990 chunk 393 optimal weight: 0.7980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1173 ASN P 262 ASN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN S 97 GLN ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.089713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.065373 restraints weight = 206471.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.066563 restraints weight = 98797.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.067113 restraints weight = 50633.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.066891 restraints weight = 47239.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.066966 restraints weight = 40958.606| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43125 Z= 0.122 Angle : 0.637 12.663 59349 Z= 0.321 Chirality : 0.042 0.343 6950 Planarity : 0.003 0.088 6736 Dihedral : 20.448 142.479 7787 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.19 % Favored : 94.55 % Rotamer: Outliers : 3.06 % Allowed : 30.20 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.12), residues: 4737 helix: 1.35 (0.11), residues: 2264 sheet: 0.18 (0.21), residues: 648 loop : -1.73 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 119 TYR 0.018 0.001 TYR A 99 PHE 0.012 0.001 PHE R 360 TRP 0.012 0.001 TRP Z 309 HIS 0.018 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (43116) covalent geometry : angle 0.63728 / 0.32 (59346) hydrogen bonds : bond 0.04213 / 2.80 ( 1947) hydrogen bonds : angle 3.89864 / 2.76 ( 5391) metal coordination : bond 0.00816 / 0.66 ( 7) metal coordination : angle 1.60316 / 0.89 ( 3) Misc. bond : bond 0.00031 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 333 time to evaluate : 1.519 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 106 ASP cc_start: 0.9318 (t0) cc_final: 0.8940 (t0) REVERT: B 93 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: B 112 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8783 (tt) REVERT: D 68 ASP cc_start: 0.7995 (p0) cc_final: 0.7663 (p0) REVERT: G 49 LYS cc_start: 0.8650 (mmmt) cc_final: 0.8293 (mmtt) REVERT: G 52 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.7168 (m-70) REVERT: G 71 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8689 (p0) REVERT: G 86 TYR cc_start: 0.5371 (OUTLIER) cc_final: 0.4935 (m-80) REVERT: M 820 TYR cc_start: 0.8861 (OUTLIER) cc_final: 0.7857 (t80) REVERT: M 837 TRP cc_start: 0.7295 (t60) cc_final: 0.7066 (t60) REVERT: M 871 MET cc_start: 0.8038 (tmm) cc_final: 0.7727 (tmm) REVERT: M 915 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8104 (mmmm) REVERT: M 988 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: M 1037 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8460 (mpt-90) REVERT: M 1053 ASP cc_start: 0.8945 (p0) cc_final: 0.8659 (p0) REVERT: M 1106 TYR cc_start: 0.7576 (p90) cc_final: 0.7166 (p90) REVERT: M 1117 ASP cc_start: 0.8704 (m-30) cc_final: 0.8348 (p0) REVERT: M 1118 MET cc_start: 0.8004 (tpp) cc_final: 0.7445 (ttm) REVERT: M 1121 PHE cc_start: 0.8897 (t80) cc_final: 0.8198 (m-80) REVERT: M 1387 ARG cc_start: 0.7199 (tpp-160) cc_final: 0.6781 (tpp-160) REVERT: P 240 LYS cc_start: 0.8765 (tptm) cc_final: 0.8167 (tttp) REVERT: P 244 ASP cc_start: 0.8816 (m-30) cc_final: 0.8531 (m-30) REVERT: P 262 ASN cc_start: 0.8508 (m-40) cc_final: 0.8170 (m110) REVERT: R 92 LYS cc_start: 0.3988 (pttp) cc_final: 0.2912 (mmtt) REVERT: R 106 MET cc_start: 0.5180 (ppp) cc_final: 0.4819 (ppp) REVERT: R 123 TYR cc_start: 0.4158 (t80) cc_final: 0.2917 (m-80) REVERT: R 199 TRP cc_start: 0.6457 (m100) cc_final: 0.5531 (t60) REVERT: R 211 LYS cc_start: 0.4731 (mmmt) cc_final: 0.4222 (tmtt) REVERT: S 102 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7431 (t80) REVERT: S 135 THR cc_start: 0.4651 (OUTLIER) cc_final: 0.4402 (t) REVERT: S 235 PHE cc_start: 0.3548 (m-80) cc_final: 0.2961 (m-80) REVERT: T 125 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8455 (t80) REVERT: U 204 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7633 (tpm170) REVERT: U 215 MET cc_start: 0.4946 (mtt) cc_final: 0.3845 (ptp) REVERT: U 221 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7428 (t80) REVERT: U 416 ASN cc_start: 0.8197 (p0) cc_final: 0.7851 (p0) REVERT: V 263 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: V 344 MET cc_start: 0.8596 (mmm) cc_final: 0.8249 (mmm) REVERT: X 406 MET cc_start: 0.8532 (tpp) cc_final: 0.8093 (tpp) REVERT: Y 23 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.7699 (p90) REVERT: Y 95 ASP cc_start: 0.6230 (t0) cc_final: 0.5965 (t0) REVERT: Y 115 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8439 (tp30) REVERT: Y 175 MET cc_start: 0.6452 (mmm) cc_final: 0.6112 (mmm) REVERT: Y 300 MET cc_start: 0.7876 (mtm) cc_final: 0.7601 (mtm) REVERT: Y 346 ASP cc_start: 0.8201 (p0) cc_final: 0.7905 (p0) REVERT: Z 196 ARG cc_start: 0.4451 (ttp80) cc_final: 0.4025 (ptt-90) REVERT: Z 216 LYS cc_start: 0.5778 (tptt) cc_final: 0.5522 (tmtt) REVERT: Z 260 LYS cc_start: 0.8034 (tppt) cc_final: 0.7458 (ptpt) REVERT: Z 263 GLU cc_start: 0.6984 (pt0) cc_final: 0.6272 (tp30) REVERT: Z 321 LYS cc_start: 0.6523 (mmtm) cc_final: 0.5794 (mmtt) REVERT: Z 588 LEU cc_start: 0.2679 (mt) cc_final: 0.2369 (mt) outliers start: 121 outliers final: 90 residues processed: 435 average time/residue: 0.2409 time to fit residues: 175.2657 Evaluate side-chains 420 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 314 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 915 LYS Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 988 GLN Chi-restraints excluded: chain M residue 994 ASN Chi-restraints excluded: chain M residue 1009 VAL Chi-restraints excluded: chain M residue 1037 ARG Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1178 ASP Chi-restraints excluded: chain M residue 1197 LEU Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1318 ILE Chi-restraints excluded: chain M residue 1328 ILE Chi-restraints excluded: chain M residue 1357 ARG Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 408 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 102 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 112 SER Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 263 GLN Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 241 LEU Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 316 LEU Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 108 SER Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 184 VAL Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 433 SER Chi-restraints excluded: chain Z residue 312 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 8 optimal weight: 0.9980 chunk 405 optimal weight: 0.6980 chunk 172 optimal weight: 5.9990 chunk 432 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 chunk 338 optimal weight: 0.8980 chunk 423 optimal weight: 3.9990 chunk 453 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1173 ASN M1309 ASN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.089200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.064981 restraints weight = 208222.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.066010 restraints weight = 103291.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.065399 restraints weight = 62412.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.066024 restraints weight = 54692.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.065889 restraints weight = 42209.386| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 43125 Z= 0.130 Angle : 0.655 13.541 59349 Z= 0.330 Chirality : 0.042 0.329 6950 Planarity : 0.004 0.089 6736 Dihedral : 20.444 142.475 7787 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.19 % Favored : 94.60 % Rotamer: Outliers : 3.03 % Allowed : 30.13 % Favored : 66.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.12), residues: 4737 helix: 1.37 (0.11), residues: 2257 sheet: 0.14 (0.20), residues: 648 loop : -1.72 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 787 TYR 0.017 0.001 TYR P 284 PHE 0.020 0.001 PHE G 68 TRP 0.029 0.001 TRP M 790 HIS 0.012 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (43116) covalent geometry : angle 0.65483 / 0.33 (59346) hydrogen bonds : bond 0.04259 / 2.83 ( 1947) hydrogen bonds : angle 3.90995 / 2.77 ( 5391) metal coordination : bond 0.00930 / 0.75 ( 7) metal coordination : angle 1.48705 / 0.86 ( 3) Misc. bond : bond 0.00089 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 330 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9303 (t0) cc_final: 0.8933 (t0) REVERT: B 93 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7704 (tm-30) REVERT: B 112 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8797 (tt) REVERT: D 68 ASP cc_start: 0.7995 (p0) cc_final: 0.7694 (p0) REVERT: E 58 TYR cc_start: 0.7870 (t80) cc_final: 0.7412 (t80) REVERT: E 62 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7620 (mt-10) REVERT: G 49 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8261 (mmtt) REVERT: G 52 HIS cc_start: 0.7677 (OUTLIER) cc_final: 0.7208 (m-70) REVERT: G 71 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8693 (p0) REVERT: G 86 TYR cc_start: 0.5274 (OUTLIER) cc_final: 0.4867 (m-80) REVERT: M 820 TYR cc_start: 0.8855 (OUTLIER) cc_final: 0.7908 (t80) REVERT: M 837 TRP cc_start: 0.7303 (t60) cc_final: 0.7051 (t60) REVERT: M 871 MET cc_start: 0.8066 (tmm) cc_final: 0.7737 (tmm) REVERT: M 915 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8090 (mmmm) REVERT: M 1053 ASP cc_start: 0.8989 (p0) cc_final: 0.8596 (p0) REVERT: M 1106 TYR cc_start: 0.7650 (p90) cc_final: 0.7252 (p90) REVERT: M 1117 ASP cc_start: 0.8771 (m-30) cc_final: 0.8467 (p0) REVERT: M 1118 MET cc_start: 0.7963 (tpp) cc_final: 0.7394 (ttm) REVERT: M 1387 ARG cc_start: 0.7154 (tpp-160) cc_final: 0.6693 (tpp-160) REVERT: P 240 LYS cc_start: 0.8774 (tptm) cc_final: 0.8187 (tttp) REVERT: P 244 ASP cc_start: 0.8800 (m-30) cc_final: 0.8497 (m-30) REVERT: P 262 ASN cc_start: 0.8556 (m-40) cc_final: 0.8288 (m-40) REVERT: R 92 LYS cc_start: 0.3935 (pttp) cc_final: 0.2815 (mmtt) REVERT: R 123 TYR cc_start: 0.4198 (t80) cc_final: 0.2876 (m-80) REVERT: R 199 TRP cc_start: 0.6480 (m100) cc_final: 0.5597 (t60) REVERT: R 211 LYS cc_start: 0.4686 (mmmt) cc_final: 0.4183 (tmtt) REVERT: S 102 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.7433 (t80) REVERT: S 135 THR cc_start: 0.4629 (OUTLIER) cc_final: 0.4381 (t) REVERT: S 235 PHE cc_start: 0.3618 (m-80) cc_final: 0.3014 (m-80) REVERT: T 125 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8492 (t80) REVERT: U 204 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7647 (tpm170) REVERT: U 215 MET cc_start: 0.5048 (mtt) cc_final: 0.3934 (ptp) REVERT: U 221 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7503 (t80) REVERT: U 416 ASN cc_start: 0.8135 (p0) cc_final: 0.7797 (p0) REVERT: V 263 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8235 (mt0) REVERT: V 344 MET cc_start: 0.8618 (mmm) cc_final: 0.8269 (mmm) REVERT: X 312 GLU cc_start: 0.7651 (tp30) cc_final: 0.7376 (tp30) REVERT: X 406 MET cc_start: 0.8633 (tpp) cc_final: 0.8260 (tpp) REVERT: Y 23 HIS cc_start: 0.8505 (OUTLIER) cc_final: 0.7693 (p90) REVERT: Y 95 ASP cc_start: 0.6426 (t0) cc_final: 0.6154 (t0) REVERT: Y 115 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8423 (tp30) REVERT: Y 175 MET cc_start: 0.6612 (mmm) cc_final: 0.6229 (mmm) REVERT: Y 300 MET cc_start: 0.7806 (mtm) cc_final: 0.7535 (mtm) REVERT: Y 346 ASP cc_start: 0.8238 (p0) cc_final: 0.7951 (p0) REVERT: Z 196 ARG cc_start: 0.4332 (ttp80) cc_final: 0.3882 (ptt-90) REVERT: Z 216 LYS cc_start: 0.5660 (tptt) cc_final: 0.5414 (tmtt) REVERT: Z 260 LYS cc_start: 0.8042 (tppt) cc_final: 0.7466 (ptpt) REVERT: Z 263 GLU cc_start: 0.6836 (pt0) cc_final: 0.6248 (tp30) REVERT: Z 321 LYS cc_start: 0.6523 (mmtm) cc_final: 0.5774 (mmtt) REVERT: Z 588 LEU cc_start: 0.2785 (mt) cc_final: 0.2180 (mp) outliers start: 120 outliers final: 95 residues processed: 431 average time/residue: 0.2484 time to fit residues: 179.0527 Evaluate side-chains 430 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 321 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 798 VAL Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 915 LYS Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 988 GLN Chi-restraints excluded: chain M residue 994 ASN Chi-restraints excluded: chain M residue 1009 VAL Chi-restraints excluded: chain M residue 1037 ARG Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1178 ASP Chi-restraints excluded: chain M residue 1197 LEU Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1318 ILE Chi-restraints excluded: chain M residue 1328 ILE Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 365 PHE Chi-restraints excluded: chain R residue 408 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 102 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 263 GLN Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 241 LEU Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain X residue 316 LEU Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 108 SER Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 184 VAL Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 417 THR Chi-restraints excluded: chain Y residue 423 VAL Chi-restraints excluded: chain Y residue 433 SER Chi-restraints excluded: chain Z residue 312 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 327 optimal weight: 2.9990 chunk 386 optimal weight: 0.1980 chunk 176 optimal weight: 0.9980 chunk 483 optimal weight: 4.9990 chunk 417 optimal weight: 3.9990 chunk 412 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 385 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 240 optimal weight: 1.9990 chunk 428 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1173 ASN ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.089344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.065427 restraints weight = 205075.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.065902 restraints weight = 117948.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.065927 restraints weight = 69272.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.065973 restraints weight = 66937.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.066064 restraints weight = 54189.869| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43125 Z= 0.125 Angle : 0.651 13.543 59349 Z= 0.327 Chirality : 0.043 0.338 6950 Planarity : 0.004 0.088 6736 Dihedral : 20.443 142.219 7787 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.02 % Favored : 94.74 % Rotamer: Outliers : 2.85 % Allowed : 30.40 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.12), residues: 4737 helix: 1.36 (0.11), residues: 2267 sheet: 0.16 (0.21), residues: 627 loop : -1.70 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 67 TYR 0.015 0.001 TYR Z 597 PHE 0.011 0.001 PHE M1308 TRP 0.017 0.001 TRP Z 309 HIS 0.019 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (43116) covalent geometry : angle 0.65068 / 0.33 (59346) hydrogen bonds : bond 0.04210 / 2.79 ( 1947) hydrogen bonds : angle 3.89381 / 2.76 ( 5391) metal coordination : bond 0.00899 / 0.73 ( 7) metal coordination : angle 1.66718 / 0.93 ( 3) Misc. bond : bond 0.00036 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9474 Ramachandran restraints generated. 4737 Oldfield, 0 Emsley, 4737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 333 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.9217 (t0) cc_final: 0.8834 (t0) REVERT: B 93 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: B 112 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8796 (tt) REVERT: D 68 ASP cc_start: 0.7893 (p0) cc_final: 0.7613 (p0) REVERT: E 58 TYR cc_start: 0.7907 (t80) cc_final: 0.7454 (t80) REVERT: E 62 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7666 (mt-10) REVERT: G 49 LYS cc_start: 0.8618 (mmmt) cc_final: 0.8243 (mmtt) REVERT: G 52 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7285 (m-70) REVERT: G 71 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8703 (p0) REVERT: G 86 TYR cc_start: 0.5301 (OUTLIER) cc_final: 0.4882 (m-80) REVERT: M 820 TYR cc_start: 0.8870 (OUTLIER) cc_final: 0.7963 (t80) REVERT: M 837 TRP cc_start: 0.7245 (t60) cc_final: 0.6991 (t60) REVERT: M 871 MET cc_start: 0.8026 (tmm) cc_final: 0.7748 (tmm) REVERT: M 915 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8103 (mmmm) REVERT: M 1053 ASP cc_start: 0.9002 (p0) cc_final: 0.8612 (p0) REVERT: M 1106 TYR cc_start: 0.7621 (p90) cc_final: 0.7217 (p90) REVERT: M 1117 ASP cc_start: 0.8793 (m-30) cc_final: 0.8466 (p0) REVERT: M 1118 MET cc_start: 0.7918 (tpp) cc_final: 0.7383 (ttm) REVERT: P 240 LYS cc_start: 0.8769 (tptm) cc_final: 0.8194 (tttp) REVERT: P 244 ASP cc_start: 0.8780 (m-30) cc_final: 0.8532 (m-30) REVERT: P 262 ASN cc_start: 0.8498 (m-40) cc_final: 0.8238 (m-40) REVERT: R 92 LYS cc_start: 0.3952 (pttp) cc_final: 0.2777 (mmtt) REVERT: R 123 TYR cc_start: 0.3979 (t80) cc_final: 0.2816 (m-80) REVERT: R 199 TRP cc_start: 0.6523 (m100) cc_final: 0.5586 (t60) REVERT: R 201 ILE cc_start: 0.8967 (tt) cc_final: 0.8251 (tt) REVERT: R 211 LYS cc_start: 0.4731 (mmmt) cc_final: 0.4148 (tmtt) REVERT: S 102 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7244 (t80) REVERT: S 135 THR cc_start: 0.4668 (OUTLIER) cc_final: 0.4394 (t) REVERT: T 125 PHE cc_start: 0.9033 (OUTLIER) cc_final: 0.8445 (t80) REVERT: U 204 ARG cc_start: 0.8110 (mmm160) cc_final: 0.7639 (tpm170) REVERT: U 215 MET cc_start: 0.5120 (mtt) cc_final: 0.4058 (ptp) REVERT: U 221 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7567 (t80) REVERT: U 416 ASN cc_start: 0.8055 (p0) cc_final: 0.7732 (p0) REVERT: V 344 MET cc_start: 0.8634 (mmm) cc_final: 0.8305 (mmm) REVERT: W 296 ASP cc_start: 0.8819 (OUTLIER) cc_final: 0.8572 (m-30) REVERT: X 224 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7154 (pp) REVERT: X 312 GLU cc_start: 0.7609 (tp30) cc_final: 0.7305 (tp30) REVERT: X 406 MET cc_start: 0.8642 (tpp) cc_final: 0.8432 (tpt) REVERT: Y 23 HIS cc_start: 0.8398 (OUTLIER) cc_final: 0.7552 (p90) REVERT: Y 60 MET cc_start: 0.8214 (ttm) cc_final: 0.7960 (mtp) REVERT: Y 95 ASP cc_start: 0.6489 (t0) cc_final: 0.6221 (t0) REVERT: Y 115 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8471 (tp30) REVERT: Y 175 MET cc_start: 0.6575 (mmm) cc_final: 0.6186 (mmm) REVERT: Y 346 ASP cc_start: 0.8251 (p0) cc_final: 0.7966 (p0) REVERT: Z 196 ARG cc_start: 0.4303 (ttp80) cc_final: 0.3856 (ptt-90) REVERT: Z 216 LYS cc_start: 0.5622 (tptt) cc_final: 0.5386 (tmtt) REVERT: Z 260 LYS cc_start: 0.8008 (tppt) cc_final: 0.7426 (ptpt) REVERT: Z 263 GLU cc_start: 0.6831 (pt0) cc_final: 0.6244 (tp30) REVERT: Z 321 LYS cc_start: 0.6536 (mmtm) cc_final: 0.5778 (mmtt) REVERT: Z 588 LEU cc_start: 0.2872 (mt) cc_final: 0.2290 (mp) outliers start: 113 outliers final: 93 residues processed: 429 average time/residue: 0.2538 time to fit residues: 182.1695 Evaluate side-chains 426 residues out of total 4184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 318 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 LYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 120 MET Chi-restraints excluded: chain C residue 65 VAL Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain G residue 52 HIS Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 86 TYR Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 835 THR Chi-restraints excluded: chain M residue 887 LEU Chi-restraints excluded: chain M residue 915 LYS Chi-restraints excluded: chain M residue 921 LEU Chi-restraints excluded: chain M residue 988 GLN Chi-restraints excluded: chain M residue 994 ASN Chi-restraints excluded: chain M residue 1009 VAL Chi-restraints excluded: chain M residue 1037 ARG Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1178 ASP Chi-restraints excluded: chain M residue 1197 LEU Chi-restraints excluded: chain M residue 1285 HIS Chi-restraints excluded: chain M residue 1318 ILE Chi-restraints excluded: chain M residue 1328 ILE Chi-restraints excluded: chain M residue 1357 ARG Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 258 VAL Chi-restraints excluded: chain R residue 365 PHE Chi-restraints excluded: chain R residue 408 SER Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 102 PHE Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 135 THR Chi-restraints excluded: chain T residue 86 THR Chi-restraints excluded: chain T residue 106 VAL Chi-restraints excluded: chain T residue 115 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain U residue 17 LEU Chi-restraints excluded: chain U residue 89 SER Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 175 MET Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 221 PHE Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 265 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 345 LEU Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 75 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 230 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 265 VAL Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 192 ILE Chi-restraints excluded: chain W residue 239 VAL Chi-restraints excluded: chain W residue 240 SER Chi-restraints excluded: chain W residue 241 LEU Chi-restraints excluded: chain W residue 283 GLU Chi-restraints excluded: chain W residue 296 ASP Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 395 SER Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain X residue 48 PHE Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain X residue 202 ILE Chi-restraints excluded: chain X residue 224 LEU Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 347 VAL Chi-restraints excluded: chain X residue 463 LEU Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 108 SER Chi-restraints excluded: chain Y residue 115 GLU Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 179 LEU Chi-restraints excluded: chain Y residue 184 VAL Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 265 ILE Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 380 SER Chi-restraints excluded: chain Y residue 417 THR Chi-restraints excluded: chain Y residue 423 VAL Chi-restraints excluded: chain Y residue 433 SER Chi-restraints excluded: chain Z residue 312 GLN Chi-restraints excluded: chain Z residue 597 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 494 random chunks: chunk 17 optimal weight: 0.0270 chunk 415 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 375 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 389 optimal weight: 6.9990 chunk 486 optimal weight: 0.0980 chunk 309 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 357 optimal weight: 2.9990 overall best weight: 0.6244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 GLN ** W 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 263 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.089603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.065491 restraints weight = 206801.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066477 restraints weight = 107752.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.066315 restraints weight = 57719.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.066471 restraints weight = 61975.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.066462 restraints weight = 51111.442| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 43125 Z= 0.118 Angle : 0.658 16.231 59349 Z= 0.328 Chirality : 0.042 0.330 6950 Planarity : 0.004 0.088 6736 Dihedral : 20.419 142.558 7787 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.11 % Favored : 94.68 % Rotamer: Outliers : 2.78 % Allowed : 30.63 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 4737 helix: 1.38 (0.11), residues: 2267 sheet: 0.18 (0.21), residues: 631 loop : -1.71 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Z 191 TYR 0.018 0.001 TYR P 284 PHE 0.024 0.001 PHE C 61 TRP 0.018 0.001 TRP Z 309 HIS 0.011 0.001 HIS Z 227 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (43116) covalent geometry : angle 0.65742 / 0.33 (59346) hydrogen bonds : bond 0.04145 / 2.74 ( 1947) hydrogen bonds : angle 3.85825 / 2.73 ( 5391) metal coordination : bond 0.00768 / 0.62 ( 7) metal coordination : angle 1.68913 / 0.96 ( 3) Misc. bond : bond 0.00036 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9679.28 seconds wall clock time: 167 minutes 11.63 seconds (10031.63 seconds total)